The Fight for Earth 2: Aliens and Avengers
by Doctor's Torchwood
Summary: The Zygons are up to no good and their plans pose a serious threat to the world. The Doctor will have to team up with his friends at SHIELD to stop them. However, SHIELD is having problems of their own. They'll need the help of the Avengers again as well. While SHIELD and the Doctor fight for Earth again, they must also watch out for the Doctor's most cunning nemesis: The Master.
1. Chapter 1

_I do not own Doctor Who, Agents of Shield, Agent Carter, the Avengers, or Guardians of the Galaxy. Only this story. This story contains spoilers for Doctor Who S8, Agents of Shield S2, and Avengers 2: Age of Ultron. Read at your own risk. This is also a sequel to my first story "The Fight for Earth". It is suggested that you read that before continuing. Also there aren't many Marvel characters in the first few chapters, but I promise more will be appearing after that. In fact, there will be connections to other areas of the Marvel Universe including Agent Carter and Guardians of the Galaxy. I hope you enjoy the story! :)_

* * *

Chapter 1

New York City, United States 1946

It was 9:00 p.m. as Connie walked down the busy Manhattan streets. The sky over New York was dark at night, but that only made the city glow even brighter. Connie was a young woman on a mission. She was once a friend of Steve Rogers before he became the famous Captain America. However, Steve died before the war was over. It seemed so strange to her that science could change a man the way it changed Steve. So, she began researching advanced science and super human technology. She soon caught the attention of Peggy Carter, a talented secret agent and former love interest of Captain America. The two women had been doing some free lance investigations recently, given that most men in their line of work deemed women as too frail for the dangerous lifestyle of a secret agent. In fact, Peggy and Connie had discovered something strange. They approached American intelligence agencies about what they discovered, but were dismissed. It was assumed that Peggy and Connie had let their imaginations run wild. So, the two women decided to find out for themselves what was going on. However, this was no ordinary human technology. They had reason to believe that what they had discovered may have been of alien origin. There were only two people in New York with extensive experience with aliens: Amy Pond and Rory Williams.

Connie had short, brown hair that she curled (as was the style of the day) and beautiful brown eyes. In fact, she looked exactly like the Doctor's current companion Clara Oswald. Connie was one of Clara's numerous echoes scattered across the universe, yet she was completely unaware of this. Peggy told Connie to meet Amy and Rory and ask them for their help. Connie continued the walk through Manhattan until she came upon an apartment building near Central Park. She calmly walked inside, through the lobby, and up four flights of stairs. Then, Connie came upon a hallway filled with doors. Behind each door lay a different apartment. She walked down the hall and stopped at the fifth door on her right. Connie then knocked on the door. Soon the door opened and a red haired woman was standing there. Connie assumed this woman was Amy Pond.

"What do you want?" Amy asked. "Do you have any idea what time it is?"

"Hello. My name is Connie." She said. "Are you Amy Pond?"

"No one calls me that." She said. "My name is Amelia Williams."

"May I come in Mrs. Williams?" Connie asked. "I've walked a mile through downtown to come and find you."

"No." Amy said. "Tell my why you're here."

"My colleague and I would like your help." Connie said.

"With what?" Amy asked.

"Aliens." Connie said.

Amy stared blankly at Connie for a moment and then said "I don't know what you're talking about."

"Yes you do." Connie said. "So does your husband. May I please come in?"

Amy stepped aside to allow Connie to enter. Amy then shut the door. Connie walked into the living room. Amy and Rory seemed to have a cozy place to live. Soon, Rory entered the room. He'd only been home for about thirty minutes after spending the whole day working at the hospital.

"Who's this?" Rory asked.

"I'm Connie." She said with a smile.

"She says she wants our help with aliens." Amy said.

"There must be some kind of mistake." Rory said.

"Save the act Mr. Williams." Connie said. "My colleague and I know about you both and about your history."

"Prove it." Amy said.

"We know about the Doctor." Connie said.

"Who is your colleague?" Rory asked.

"Agent Peggy Carter." Connie said. "We do a lot of freelance investigating. We'd like your help with a case. It's like nothing we've encountered before."

"How do you know about us and the Doctor?" Amy asked.

"You all pop up throughout history." Connie said. "When you do, people write them down. Vincent Van Gogh wrote about you. Winston Churchill wrote about you. Hitler wrote about you. All these texts have been hidden and locked away, but they can be found if you know where to look. I'm sure you also remember Mercy, Nevada. There's a ninety year old woman there who still remembers what happened with you and the Doctor and the Kahler robots back in 1870."

"What's the problem?" Rory asked. "How do you know it's aliens?"

"We don't." Connie said. "Neither Peggy nor I have encountered them before. That's why we want your input."

"Why didn't this Agent Carter come meet us herself?" Amy asked.

"People in this city know her and they know me. We didn't want to draw too much attention." Connie said. "Would you come with me to the Empire State Building? Peggy is waiting there for us."

"Can't we do it in the morning?" Rory asked.

"I'm afraid not." Connie said. "More people will keep going missing the longer we wait."

"People are going missing?" Amy asked.

"Yes." Connie said. "Peggy will tell you everything when we get to her. Will you come with me?"

"Yes." Amy said.

* * *

London, England 2015

It was a sunny morning in London. Martha Jones, Mickey Smith, and Jack Harkness had embarked downtown on their way to U.N.I.T. headquarters in the Shard, London's tallest skyscraper. Martha, Mickey, and Jack were made honorary S.H.I.E.L.D. agents by Nick Fury himself after they helped save the planet from the double invasion of Daleks and Chitauri alongside the Doctor, Clara, River Song, the Avengers, and Agent Coulson's S.H.I.E.L.D. team. However, since it became known that H.Y.D.R.A. had infiltrated S.H.I.E.L.D., the three of them laid low in London, doing what they could to fight H.Y.D.R.A. underground. The previous night, they found Clara Oswald crying on a bench near Big Ben. She had told them that the Doctor took her to the Himalayas in 1992, where he was killed by Zygons. She said that the TARDIS took her home and then disappeared with the Doctor's body still inside. Martha was skeptical of this story. So, Clara said that they could ask U.N.I.T. because every time the TARDIS lands on Earth, U.N.I.T. has a file on it. Martha, having worked at U.N.I.T., knew that they did keep accurate records of the Doctor's visits to Earth. On this day the three of them were walking to U.N.I.T. to confirm or disprove Clara's story that the Doctor was dead.

Unbeknownst to them, it was not Clara Oswald that they had spoken to last night. In fact, it was one of two crafty Zygons based in London, who wanted three time travelers to go to U.N.I.T. for their own purposes. Also unbeknownst to Martha, Mickey, and Jack was that today was a monumental day at U.N.I.T. The Doctor(s) and Clara Oswald recently discovered that Zygons, in order to escape the destruction of their homeworld by the Time War, used Gallifreyen technology to trap themselves in paintings that were now held in the National Gallery. Some Zygons has escaped and were planning on releasing the rest of their species. The Doctor convinced U.N.I.T. and the Zygons to negotiate. After multiple scheduling conflicts, U.N.I.T. and the Zygons who had left the paintings were finally going to conference about what to do next. Martha, Jack, and Mickey walked into U.N.I.T. and found Kate Stewart pacing as she walked through the lobby. Kate stopped when she saw Martha, Mickey and Jack. Confused, she decided to talk to them.

"What are you all doing here?" She asked.

"Hello mam." Martha said. "We need to ask you some questions."

"I don't have time." Kate said. "I've got to begin negotiations with the Zygons in twenty minutes."

"It's about the Doctor." Mickey said.

"Isn't it always?" Kate sarcastically asked. "You'll have to come back some other day."

"He's dead." Jack said.

"Sure he is." Kate said. "Of course he is. Why wouldn't he be? Except for that he isn't. This is not the first time we've been told that the Doctor is dead only to find out that he's been alive and well the whole time."

"Can you check your records?" Martha asked. "The Himalayas. 1992."

"Not today." Kate said. "I'm sorry, but I have to go. I suggest you leave."

Kate the walked away from them. Suddenly, a soldier in a U.N.I.T. uniform came up to them.

"I can help you." He said. "You want to know what happened to the Doctor. Follow me."

"Your boss just told us to leave." Mickey said.

"She is very busy today." The soldier said. "She wants to help, but she does not have time. She would want me to show you."

"Alright then." Martha said. "Let's go."

The soldier led them through the crowded building and into an empty elevator. They rode the elevator all the way to the very bottom floor of the building. They stepped out into an empty hallway with one door at the very end.

"What's down here?" Jack asked.

"The answer to your questions." The soldier said.

They walked down the hall and opened the door. Inside was a small, white room filled with three chairs that one may find in a dentist's operating room. At the end of each chair was a wire that connected to a yellow sphere in the far left corner of the room. However, that was not the most surprising thing in there. There was a man waiting for them. It was the Doctor. However it was not the right Doctor. This was the spikey haired Doctor from his tenth incarnation. However, the Doctor that had helped them stop the Dalek-Chitauri invasion was in his eleventh incarnation.

"Hello." The tenth Doctor said.

"Something's not right." Martha said.

The soldier shut the door once everyone had stepped inside and locked it.

"I told you that's not what he looks like." The soldier said.

"This is how he looked in 1946." The tenth Doctor said.

"No." The soldier said. "It's like this."

The soldier's body then began to morph and twist and reconfigure. Within seconds, the soldier was no longer there. He had metamorphosed into the Doctor in his twelfth incarnation, which Martha, Mickey, and Jack had never seen before.

"How was I supposed to know that?" The tenth Doctor asked.

"Remember the Himalayas in 1992?" The twelfth Doctor asked. "This is what he looked like."

"What's going on here?" Mickey asked.

The two Doctors looked at each other. Then, they both started to morph again. This time, their skin turned dark red. They started to grow slightly taller and suction cups formed over their bodies. They were not humans. Martha Jones, Mickey Smith, and Jack Harkness were now trapped in a room with two evil Zygons.


	2. Himalayas

Chapter 2: Himalayas

Himalayan Mountains, Nepal 1992

The TARDIS materialized high on a snowy mountain surrounded by rocks. The Doctor in his twelfth incarnation stepped out with Clara Oswald following him. Each was wearing a winter coat to protect themselves from the intense cold. The Doctor and Clara were just leaving the Orient Express, a space train haunted by a mummy, when they suddenly received an alert from the TARDIS. On the viewing screen, the TARDIS said that there was an emergency in the Himalayas. The Doctor and Clara both decided to investigate.

"What's the emergency?" Clara asked.

"I don't know." The Doctor replied. "Let's go find out."

"Look around." Clara said. "These mountains are dangerous. We can't just go frolicking about until we find danger. People die up here. Besides, this place is massive. How are we supposed to know where to look?"

"Hello!" A male voice called out to them.

The Doctor and Clara turned to the right to find the silhouette of a man waving at them in the distance.

"We'll just ask him." The Doctor said.

The Doctor and Clara ran across the treacherous rocks until they came face to face with this strange man. He was as tall as the Doctor, but he was young, around Clara's age and had red hair and freckles.

"Thank goodness we found you." The man said. "We need to get you to safety."

"Why?" The Doctor asked.

"I came here with my wife to climb this mountain. We heard news that a couple had disappeared on the trek a few days ago. My wife and I decided to look for you on our way up. I'm so happy we found you." The man said.

"What's your name? Clara asked.

"Oliver." He replied.

"Well Oliver." Clara said. "We aren't that couple. In fact we're not even a couple. We're just friends. Best friends. That's all. I actually do have a boyfriend back home."

"All I know is that two people went missing up here a few days ago. You're not them?" Oliver asked.

"I'm afraid not." The Doctor said.

"Are you climbers too?" Oliver asked.

"Sure." The Doctor said. "If you don't mind we have to go back to our...tent now."

"What's your name?" Oliver asked.

"I'm Clara." Clara said. "And this is the Doctor."

"The Doctor?" Oliver asked. "It can't be you. Are you a time traveler."

"How can you know that?" The Doctor asked.

"My wife is part of an online conspiracy theory blog sort of thing. The Doctor is mentioned constantly. Can you come back to our tent? She'd love to meet you." Oliver said.

"Fine." The Doctor said. "Lead the way."

"Is that really a good idea?" Clara whispered to the Doctor.

"These people clearly know things we don't." The Doctor whispered back to her. "The TARDIS wanted us to come here for a reason. Maybe they know what it is."

"He just said people went missing." Clara said.

"So we'll just have to be careful." The Doctor said.

Oliver led the Doctor and Clara through the snow and rocks for a few minutes until they came upon a large, dark cave.

"This is where we stayed last night." Oliver said. "When nature provides a shelter for you, why would you pitch a tent?"

Oliver pulled out a flashlight from his coat pocket and shined it into the cave. The Doctor and Clara saw nothing.

"There's no one in there." The Doctor said.

"We're staying deep in the cave." Oliver said. "We figured we wouldn't be as cold that way."

Oliver then entered the cave using his flashlight to lead the way.

"Don't you think this is a little bit suspicious?" Clara asked the Doctor. "People are going missing and the only other person here lives in a dark cave."

"I know Clara." The Doctor said. "I'm not an idiot. We're going to follow him and see what we can find out."

The Doctor and Clara followed Oliver for about a minute, until they became perplexed. Oliver's flashlight was shining on a white, metal door in front of them.

"I know it appears odd." Oliver said. "My wife and I have been living behind this door."

"You brought a door al the way through these mountains?" The Doctor asked.

"Yes." Oliver said. He then opened the door and walked inside.

The Doctor and Clara nervously followed. Inside was a small, white room filled with two chairs that one may find in a dentist's operating room. At the end of each chair was a wire that connected to a yellow sphere in the far left corner of the room. Standing at the other side of the room was a woman with red hair.

"This is my wife." Oliver said, as he walked over to the woman and stood next to her. "Welcome to our home. If you'll just have a seat we'll get you some tea."

"No." The Doctor said. "Do you think I'm stupid. Did you think I wouldn't be able to figure out what's happening here?"

"What is happening here?" Clara asked.

"They want our time energy." The Doctor said.

"Time energy?" Clara asked.

"It's harmless." The Doctor sad. "Just something you pick up while traveling through the time vortex. They want to strap us into those chairs and absorb it into that yellow sphere. I've seen this before. It happened long ago before the Time War. How did you even get this technology?"

"Very perceptive." Oliver said.

Oliver's body then began to morph and change. His body became red, he grew taller, and suction cups formed on his body. Oliver was a Zygon. His red haired wife also started to change and in seconds, she too had transformed into a male Zygon.

"Zygons." Clara said.

"Very perceptive, Clara." The Zygon posing as Oliver said.

"I take it your name isn't Oliver." The Doctor said. "What is it?"

"My name is Jim." The Zygon said. "My brother's name is Tim."

"We adopted human names when we fled our planet to hide on Earth." Tim said.

"What do you need time energy for?" Clara asked.

"That's not your business." Jim said. "It's ours. Now get in the chairs before we make you."

"You've got quite the family operation going on here." The Doctor commented.

"You have no idea." Tim said.

"How many of you are there?" Clara asked.

"Right now it's just us." Jim said. "My children will be arriving soon. Now sit!"

The Doctor whipped out his sonic screwdriver and held it high above his head. Then, he activated the device, creating a sonic noise that pierced the Zygon's ears and made them scream and fall to their knees. The Doctor and Clara were unaffected.

"Run!" The Time Lord yelled.

The Doctor and Clara turned around and started to run out of the cave. Once they left the room, the Zygons could no longer hear the noise.

"Get them!" Jim yelled.

The two Zygons then started to run after them.

It was dark in the cave. The Doctor and Clara could hear the Zygons running somewhere behind them, but they could not see. It reminded them of the time they were running from a Cyberman in the darkness of the New York City subway tunnels. That was the day they met Agent Coulson and his S.H.I.E.L.D. team, including Agents May, Skye, Ward, Fitz, and Simmons. They'd become good friends with that team and the Avengers while they fought to save the Earth from the Chitauri and the Daleks. Yet there was no time to focus on that now. They had to get out of this cave and escape the Zygons. The Doctor and Clara could see the light of the outside growing wider and brighter as they ran closer. The Doctor then had an idea. He kept his sonic screwdriver in hand. When the Doctor and Clara finally reached the end of the cave, Clara kept running back to the TARDIS. However, the Doctor stopped and turned around. He pointed his sonic device at the top of the cave. Then, he activated it. Simultaneously, the top of the cave began to crack and break. Rocks from the cave ceiling fell to the ground, blocking the entrance, and trapping the Zygons inside. The Doctor then ran back to the TARDIS with Clara and left the Himalayas, believing the Zygons to be dead.

* * *

One hour later...

The Doctor's plan had not killed the Zygons. It only trapped them. The two of them worked together and moved enough of the rocks out of the way in order to get out of the cave. The Zygons then discovered that the TARDIS had left a long time ago, taking the Doctor and Clara Oswald with it.

"What do we do now?" Tim asked.

"We wait." Jim said.

"We've been waiting for over four hundred years." Tim said. "They only way to avenge your wife is to bring your children back."

"You think I don't know that?" Jim asked. "You think I don't want to see my own children? Go back to the cave and pack up. We need to get back to Russia. I'll call and tell her the plan failed."

"She won't be happy." Tim said.

"I know," Jim said, "but she will understand. The reason she's working on a plan B, is just in case this one doesn't work, which it doesn't seem to be. She needs to know that we may have to call her in if we can't find any time energy."

"Fine." Tim said.

Tim went back into the cave, while Jim stayed out on the snowy mountain. He was wearing an alien wrist communicator. He held his wrist up towards his face, pressed in some numbers, and waited.

* * *

Afterlife, 1992

Jiaying walked down the outside path of her community of inhumans on a beautiful sunny day. She'd spent much of her recent life creating this place and recruiting inhumans, people with superhuman abilities, to teach them how to become who they were meant to be. It was early. She had woken up to watch the sunrise. No one else was awake yet. Jiaying was wearing a wrist communicator and heard it beep. She held it up to her face and pressed a button.

"Did everything go as planned with the Doctor?" Jiaying asked into the device.

"No." Jim the Zygon replied.

"This is not good." Jiaying said.

"I know." Jim said. "What progress have you made in finding the inhumans?"

"We're still pretty small." Jiaying said.

"It's much harder than we thought to find those who have traveled through the time vortex." Jim said. "We may have to resort to plan B."

"Plan B is not ready yet." Jiaying said. "I need more inhumans if plan B were to even have a shot at being successful."

"Tim and I are going back to Russia." Jim said. "We'll talk to you again when we get there."

Jiaying then hung up on her Zygon allies and watched the sun rise. Suddenly, a flash of blue light appeared. Then, a tall man with no eyes stood in front of Jiaying.

"I found another one in Morocco." The man said.

"Excellent Gordon." Jiaying said. "How soon can you get them here?"

"I'll have to talk with him first." Gordon said.

"Of course." Jiaying replied. "I look forward to our next addition."

* * *

"What did the Zygons want with time energy?" Clara asked as she and the Doctor moved about the TARDIS.

"I have no idea." The Doctor said.

"Well they should be dead now." Clara said.

An alarm suddenly started to sound throughout the TARDIS. The Doctor and Clara went up to the viewing screen on the TARDIS console to see what was happening.

"It's another Zygon emergency." The Doctor said. "This time it's in London at the U.N.I.T. headquarters in 2015. That's when Kate is supposed to be having negotiations with those Zygons who were in the paintings."

"Coincidence?" Clara asked.

"Let's go and find out." The Doctor said.


	3. Agent Carter

Chapter 3: Agent Carter

New York City, United States 1946

It was the middle of the night in the city that never sleeps. One of Clara Oswald's time echoes, Connie, a freelance investigator working closely with Agent Peggy Carter, had successfully convinced Amy Pond and Rory Williams to go to the Empire State Building and meet with Peggy. Amy and Rory had been stuck in 1940's New York for about a year now after they were sent there by a Weeping Angel. They had to remain there to avoid a paradox. In the future, they saw their graves in a New York City graveyard. If they were to ever leave the city and die somewhere else, it was unlikely they would be buried in New York, causing a paradox. New York had been the epicenter of many paradoxes before. If a new one were to be introduced, it would have catastrophic effects. So, Amy and Rory tried their best to stay in the city. Now, they walked with Connie to the Empire State Building to meet Agent Carter and discuss a possibly alien problem she'd discovered. They approached the building, but did not walk inside. Connie was leading them to an alley next to the building. Inside this dimly lit alley was a single woman, Agent Carter.

"Hello." She said as she approached Amy and Rory. "I'm Peggy Carter. I'm sure Connie's told you something about me."

"Not really." Rory said.

"You're from England too?" Peggy said, noting Rory's accent. She knew about Amy and Rory's adventures with the Doctor, but she assumed they were American because they lived in New York.

"He is." Amy said. "I'm from Scotland."

"Thank you for coming." Peggy said. "I know it's late. We don't have time to lose."

"We were told there was something alien going on." Amy said.

"We think so." Connie said. "We're not sure."

"So what is it?" Rory asked.

"In the day, I work for the S.S.R." Peggy said. "They picked up strange readings in Moscow, unlike any they'd seen before. They didn't know what to make of it, but because it's the heart of the Soviet Union, they couldn't investigate much further. That same day a new painting went on display at The State Tretyakov Gallery in Moscow. It's an esteemed art museum. Then we started getting reports of people going missing in the museum. They had to temporarily close the it, but they still keep security guards roaming the place. Then, we got reports that the security guards were going missing too. All this happened after we got strange readings and a new art piece came to the museum."

"That's not the weirdest thing I've ever heard of." Rory said. "It could be alien."

"That's what I think." Peggy said. "The boys at the S.S.R. wouldn't believe me. So I asked Connie to help me look into it. Then we tracked you down."

"So what do you want us to do?" Amy asked. "The possible aliens are in Russia."

"Exactly." Peggy said. "Connie and I are planning to go there tomorrow. We'd like you to join us. You have more alien experience then either of us. You may even know who is making all the people disappear."

"We can't leave New York." Rory said.

"Why not?" Connie asked them.

"It's a long story." Rory said. "We just can't."

"We absolutely can." Amy said. "We can leave any time we want. We just can't die anywhere but here. Can you guarantee that we won't die?"

"Could the Doctor guarantee you wouldn't die?" Peggy asked. "I doubt it, but that never stopped you."

"That was when it was just our lives on the line." Rory said. "I can't explain it all, but know that if we die outside this city, millions will die."

"I can't make you go,' Peggy said, "but I can tell you that we'll figure this out faster and likely save millions of lives if you do go."

"We'll do it." Amy said.

"Amy!" Rory said.

"We never have any adventures anymore." Amy said.

"You said you were ok with that." Rory reminded her.

"I am," Amy said, "but there's a part of me that misses traveling with the Doctor. I know you feel that way too. We'll just have to be careful. We'll be together and we'll be with some of the most skilled agents in America."

"What do you say Rory?" Peggy asked.

Rory thought it over for a brief moment. "Fine." He said. "I guess it could be fun."

"Great." Peggy said. "You can go back to your apartment now and get some rest. I have a few favors to call in. Tomorrow, we're going to the Soviet Union to look into aliens."


	4. The Doctor Returns part 1

Chapter 4: The Doctor Returns part 1

U.N.I.T. Headquarters, London, England 2015

Martha Jones, Jack Harkness, and Mickey Smith looked fearfully at the two Zygons that had just trapped them in an underground facility beneath U.N.I.T. Headquarters. One stood at the door and one stood at the opposite side of the room in front of three dentist style chairs with wires connected to a yellow sphere.

"What the hell are they?" Mickey asked, unfamiliar with this particular alien life form. Martha did not know either.

"Zygons." Jack said. "They're shape shifters."

"What do you want?" Martha asked.

"We want you." One of the Zygons said. "Isn't that obvious? That's why Tim got you to come here."

"Tim?" Jack asked.

"Me." The Zygon by the door said. "My brother's name is Jim."

"I bet that wasn't Clara we talked to last night then." Martha said.

"Correct." Jim said. "It was my brother in a clever disguise."

"Is the Doctor really dead?" Mickey asked.

"Unfortunately no." Jim said. "He's just difficult to catch. That's why we've settled for you three."

"Why?" Jack asked.

"So I can see my children again." Jim said.

Then, Jim pulled out a small laser gun that was sitting on the floor behind him. Martha, Jack, and Mickey were all too focused on figuring out what was happening to notice the weapon at first. Jim the Zygon aimed it at the three former time travelers. He pulled the trigger, but instead of firing a deadly laser, it fired a pink gas. Almost immediately upon impact, Martha, Mickey, and Jack smelled the gas and fainted. After a few seconds, the gas disappeared completely.

"Let's get them in the chairs." Tim said.

* * *

Jack awoke sometime later in the same room. However, he now found that he was sitting in one of the chairs and that his arms were strapped down. He couldn't get up. He looked to his left and saw Martha and Mickey unconscious in the other two chairs.

"Good morning sunshine." Jim the Zygon said as he walked into Jack's line of sight. Jack saw that the Zygon was now holding the yellow sphere in its hand. It was about the size of a baseball.

"What did you do to us?" Jack asked.

"We took your time energy." Tim said as he too walked into Jack's line of sight. "You three have all traveled through the time vortex. U.N.I.T.'s files say you were all former companions of the Doctor. Therefore, you have time energy, so we took it."

"The orb absorbed all of it." Jim said.

"Why?" Jack asked.

"Because this world isn't big enough for the both of us." Jim replied. "You may know that Kate Stewart is currently debating with Zygons upstairs about what to do now that our Zygon leaders have come out of their paintings."

"Let me guess." Jack said. "The Zygon leaders hired you two to kill all humans while we aren't paying attention."

"No." Tim said. "They hate us. The Zygons Kate Stewart is talking to are the leaders and politicians. They labeled us as criminals long ago."

"We've been here a long time, waiting for this moment." Jim said.

"Why am I so weak?" Jack asked.

"Your time energy is a part of you." Jim said. "We've just extracted it. You shouldn't even be awake. It should take you a few days to recover."

"I recover quicker than most people." Jack said. "You won't get away with this."

"Even if you're right and we don't get away with this," Jim said, "we have a plan B. We are going to take this planet and there's no one who can stop us."

Suddenly, there was a breeze in the room, which was odd because they were deep underground and the door was shut. Then, Jack and the two Zygons heard a loud wheezing type sound that they had all heard before. It was the unmistakeable sound of the Doctor's time machine. If anyone could stop the Zygon's, it was the Doctor, who was now arriving. Jack felt relieved. Jim and Tim stared angrily at the forming TARDIS, which neither of them had seen since 1992.


	5. Welcome to Russia

Chapter 5: Welcome to Russia

New York City, United States 1946

It was 9:00 a.m. in New York. Amy and Rory had walked into an apartment building that was not their own and climbed up the stairs on their way to see Agent Peggy Carter and her assistant Connie, an echo of Clara Oswald. They had agreed to go with Peggy and Connie to Moscow to look into possible alien activity at an art museum where people were going missing. They finally found the door to Peggy's apartment and knocked on it. Connie answered the door and invited them inside. Peggy was waiting for them. She said she had one last call to make before they left. She offered them tea, as per British custom, which Amy and Rory both missed having lived in America for so long. They graciously accepted. Amy and Rory sat at Peggy's kitchen and drank their tea. After a few moments, they blacked out.

* * *

The Skies of Western Russia 1946

Amy awoke slowly. The last thing she remembered was drinking tea at Peggy Carter's apartment in New York. Now, as she gazed around it became clear that she was no longer there. Amy was sitting on a bench. In fact she was strapped in with a seatbelt. She leaned back and found that there was a wall behind her. Agent Carter and Connie were sitting directly across from Amy. They were fully awake and also strapped to a bench with a black wall behind them. She looked to her right and saw her husband next to her, still asleep. Amy then figured out where she was. She and Rory were on a military plane and they were flying through the air. Amy could tell by the sudden bouncing of the plane and she could vaguely see clouds outside of the plane's few windows. It was apparently night. She and Rory must have been knocked out the entire day, or perhaps only a few hours, if they were in a different time zone.

"You drugged us." Amy said to Peggy and Connie.

"I had to." Peggy said. "The people flying this plane don't want anyone to know about them. We'll be flying over Moscow in a few minutes."

"You mean we'll be landing in Moscow in a few minutes." Amy said.

"No." Peggy said.

"Once we're over the drop sight, they'll open the back door and we'll all jump out." Connie said. "There are parachutes on the floor that we'll be using."

Amy then used her right arm to shake her husband awake.

"What's going on?" Rory asked.

"We're on a plane." Amy said. "We're about to fly over Moscow. We're going to put on those parachutes and jump down to the city."

"I never got to finish my tea." Rory said.

"Some other time." Peggy said. "Find out what's going on in Russia. Then, we'll get tea."

"Who's flying the plane?" Rory asked.

"I can't tell you that." Peggy said. "You meet a lot of people in my line of work. Not all of them want their names out there."

"How are we going to get back home when we're done?" Rory asked.

"I'll call them again." Peggy said. "They'll pick us up."

The plane's back door started to automatically open slightly.

"That's our cue." Connie said.

Everyone then unbuckled their seat belts and carefully put on their parachutes. When they finished, the door opened the rest of the way. Even though it was night and partially cloudy, they could see the city below them. It was the largest city in Russia and one of the largest in all of Europe. Now, Agent Carter, Connie Oswald, Amy Pond, and Rory Williams were about to jump into it in order to investigate the possibility of aliens. One by one, they jumped from the plane and descended into the outskirts of Moscow where no one would see them land.

* * *

Moscow, Soviet Union 1946

Peggy, Connie, Amy, and Rory successfully landed outside Moscow unnoticed. They spent they next hour walking at night and sneaking around until they were in downtown Moscow. They were looking for The State Tretyakov Gallery, an esteemed art museum that was temporarily closed due to all the strange disappearances there of civilians and security guards following the introduction of a new painting to the museum. After walking for about thirty minutes downtown, they finally found it. The building was not incredibly tall, but was still vast in size. The entrance was not particularly ornate with a simple red and white pattern on the walls and uniquely Russian architecture that made up the wooden doors, which were locked.

"If only we had a sonic screwdriver." Amy said to Rory.

"It wouldn't help." Rory said. "It doesn't work on wood."

Peggy pulled out a small gun from her coat pocket and shot the door's keyhole, unlocking it. She, Connie, Amy, and Rory then walked inside. The inside was dark. There were no people inside. All the paintings and sculptures across the building remained untouched.

"If there are aliens here, they clearly don't care about art." Connie said. "They haven't touched anything."

"Let's not jump to any conclusions yet." Peggy said. "We came all this way. We need to look around more."

"Where's the new painting?" Amy said. "We should start by having a look at that."

"It should be just this way." Peggy said as she marched forward with Connie, Amy, and Rory following her.

Peggy led them down a hallway with beautiful paintings on the walls until she stopped at one of them. The painting didn't look like anything alien. It was a forest. There were no animals. Only multiple, trees and a few beams of sunlight shining through.

"Are you sure this is it?" Rory asked. "I don't see anything alien about it."

"It's just a bunch of trees." Amy said, remembering the time that she was trapped in a forest with a Weeping Angel.

"Hey!" A masculine voice called from the other end of the hallway. The four of them turned to see a man dressed in a security guard uniform staring at them. He said something in Russian, but no one could understand him. Amy and Rory missed the easiness of the TARDIS translation matrix. The guard could tell that they could not understand him. So, he said something else, this time in French. Still, he got no response from the intruders. Finally, in English, he said, "No one is allowed in here. You are trespassing. Get away from that painting."

"You're not supposed to be here either." Peggy said. "This building is off limits to everybody, including security guards."

"You don't know what you're talking about." The man said.

"Who are you?" Amy asked the man.

He did not answer. Instead, his body started to shake. Then, his entire body, including his clothes, started to morph and change. Soon, he grew taller, his skin turned red, and he was covered in tiny suction cups. Amy and Rory recognized this creature as a Zygon. The Doctor once took them to the opening of the Savoy Hotel in London in 1890 only to discover that half the staff were actually Zygons. They managed to stop them then and wondered what one was doing in Russia guarding a painting. Suddenly, two more Zygons appeared at the other side of the hallway such that now Peggy, Connie, Amy, and Rory were trapped in a hallway with Zygons at both ends.

"Well we were right." Connie said. "It was aliens."


	6. The Doctor Returns part 2

Chapter 6: The Doctor Returns part 2

U.N.I.T. Headquarters, London, England 2015

In a secret underground room at the U.N.I.T. Headquarters in London, Jack Harkness, Mickey Smith, and Martha Jones lay on three chairs. Their time energy was extracted by two criminal Zygons for their own purposes while the good Zygon politicians debated terms of release from their paintings with Kate Stewart and U.N.I.T. upstairs. The two criminal Zygons, Jim and Tim, were excited that they finally had enough time energy to go through with their plans. However, the TARDIS had started to form inside the room. The Doctor and Clara Oswald were preparing to step out and fight the Zygons. Anticipating this, the two Zygons ran out of the room, holding the yellow sphere that contained the stolen time energy. After they left, the TARDIS finished materializing. The twelfth Doctor and Clara stepped out and were shocked to find their friends Jack, Mickey, and Martha strapped to dentist chairs and unconscious. It looked like the same room from the Himalayas in 1992, when the Zygons tried to take the Doctor and Clara's time energy.

"Doctor?" Jack asked. Evidently he was awake, but he was very weak.

"Jack." The Doctor said as he ran over to him and started to loosen the straps that bound Jack to the chair. "What happened?"

"You regenerated again." Jack said. "I knew you weren't dead."

"Yes I know. I was there." The Doctor said. "Can you tell us what happened?"

"Zygons." Jack said.

"Let me guess." Clara said. "Their names were Jim and Tim."

"How did you know that?" Jack asked.

"We were just at the Himalayas in 1992." Clara replied. "Those same Zygons brought us to a room like this and tried to take our time energy, but we escaped."

"That was twenty three years ago." The Doctor said. "Did they take your time energy?"

"Yes." Jack said. "Martha and Mickey are out cold. I'm only awake because I heal faster than most people."

"Where are Jim and Tim now?" The Doctor asked.

"They left with the time energy when they saw the TARDIS start to form." Jack said.

"It's no use running after them." The Doctor said. "They could've changed into anyone by now."

"Doctor." Jack said. "There's something else you should know. Jim and Tim are criminal Zygons. There are innocent, nice Zygons debating with Kate Stewart about paintings or something. Those are the good guys. Jim and Tim made it very clear that they're acting separately."

"Then we can't tell anyone at U.N.I.T. about this." The Doctor said. "It would ruin negotiations."

"There's more." Jack said. "They said they wanted to take over the planet and that even if their plan with the time energy failed, they still had some kind of a plan B."

"What about Mickey and Martha?" Clara asked. "We can't just leave them here."

Clara was remembering her adventures with Martha Jones and Mickey Smith from the previous year. While the Doctor was away, she teamed up with Martha, Mickey, and S.H.I.E.L.D to recruit the Avengers and stop a dual invasion of Chitauri and Daleks. In fact, the last time she was in London with Martha and Mickey, they were fighting aliens after recruiting Bruce Banner aka The Hulk.

"We'll get them into the medical facility inside the TARDIS. They can rest there for a few days." The Doctor said. "We have to focus on the Zygons now."

"If they have a plan B," Clara said, "then maybe we shouldn't go after them alone, especially since they're shape shifters. We may need some help."

"From who?" The Doctor asked. "We can't ask U.N.I.T."

"We can ask S.H.I.E.L.D. and the Avengers again." Clara said. "We worked well together last time."

"That's the best idea you've had all day." The Doctor said.

"Doctor." Jack said. "S.H.I.E.L.D. was disbanded after it as revealed that H.Y.D.R.A. agents had been infiltrating the agency for years."

"Yes I know." The Doctor said. "Agent Coulson is still running the organization underground."

"There's something else you should know." Jack said. "Awhile ago, there was a pretty nasty earthquake in San Juan, Puerto Rico that S.H.I.E.L.D. was involved with. That's all I know about it."

"It just so happen to know where Coulson is." The Doctor said. "We'll get Martha and Mickey in the TARDIS and go see him."

"Can I go with you?" Jack said. "I'm healing very quickly and I don't want to just sit around while the world is in peril. Besides, it'll be nice to see our S.H.I.E.L.D. friends again."

"Fine." The Doctor said.

"I'll call a friend and ask her to research what she can about the Zygons on Earth." Jack said.

"It's not exactly something you can just google." Clara said sarcastically.

"She's resourceful." Jack said. "She used to work with me at Torchwood before that was disbanded."

"Alright," The Doctor said, "but help us get Martha and Mickey in the TARDIS first."

The Doctor, Jack, and Clara spent the next few minutes carrying Martha and Mickey through the halls of the TARDIS into two beds in the medical facility there. Then, Jack made a call to his old friend Gwen Cooper, who agreed to research whatever she could on the Zygon creatures. The Doctor then set a course for Agent Coulson's office at the new S.H.I.E.L.D., knowing that they needed his help in order to defeat the two criminal Zygons before they conquered the planet. However, S.H.I.E.L.D was already involved with another battle in Sokovia in Eastern Europe.


	7. Zygon Plans Revealed

Chapter 7: Zygon Plans Revealed

Moscow, Soviet Union 1946

Agent Peggy Carter, Connie Oswald (an echo of Clara Oswald), Amy Pond, and Rory Williams stood still inside one of Russia's premier art galleries. They came here at night to investigate strange disappearances in this museum after a new painting was introduced. They found this painting to be simply one of a forest. There were no animals or people, only trees. They glanced at this painting in the center of a long hallway. They couldn't discover what was strange about it until three Zygons arrived to defend the painting. One Zygon stood at one end of the hallway, while the other two stood at the other end. Amy and Rory recognized the Zygons from a previous adventure with the Doctor.

"Watch out." Rory said. "They're Zygons. Alien shape shifters."

"So what do they want with a painting of a forest?" Connie asked.

The Zygons roared at the four intruders.

"Shut up!" Amy yelled, silencing the Zygons.

"What are you doing here?" Peggy asked.

"We don't have to answer to you!" One of the Zygons said.

"Then answer me!" Amy yelled. "I know about you."

"Prove it." Another Zygon said.

"You're called Zygons." Amy said. "You're planet was destroyed in the Time War between the Time Lords and the Daleks many years ago."

"Daleks?" Peggy said. "How?"

"You know about the Daleks?" Rory asked.

"Five years ago," Peggy said, "when the Germans were still bombing London, Winston Churchill had a few Daleks fighting for the British, or so he thought."

"I know." Amy said. "I was there."

"How can you have such knowledge of us and our home world?" The third Zygon asked.

"Ever heard of the Doctor?" Amy asked, knowing that they must have. "That's how I know. So tell me what you're doing here, why this painting is so important, and why people in this museum have been disappearing."

"I suppose we should." One of the Zygons said. "The last thing she hears before she dies will be of our victory."

"What are your names?" Rory asked. "How can we tell you all apart?"

"My name is Tim." The one Zygon at the end of the hall said.

"I am Jim." One of the two Zygons to the other end of the hall said.

"I am Jim's wife Michelle." The other Zygon at the other end of the hall said. "We adopted human names when we came here."

"Which was when?" Connie asked.

"1562." Tim said.

"Start from the beginning." Peggy said.

"The Time War destroyed our home planet." Tim said. "So the Zygons came to Earth in 1562 and used Time Lord technology to hide inside paintings. They plan on coming out in the twenty first century, when your technology greatly improves."

"What about you?" Rory asked. "You're talking about other Zygons in England. What are you doing here in Russia?"

"Those Zygons who engaged Queen Elizabeth in England were the leaders, the politicians, the doctors, the scientists, and so on." Jim said. "My brother, my wife, myself, and our children are what you would call criminals."

"They wouldn't let you in the paintings with the rest of the Zygons because you're convicts." Amy said.

"Correct." Michelle said. "So, we stole our own Time Lord technology and put our children in that painting of a forest."

"That was hundreds of years ago." Connie said. "How are you still alive?"

"Our life spans are much longer than yours." Tim said.

"Why did you put your children in paintings and not yourselves?" Peggy asked.

"We wanted to be sure the painting would be protected over the years and not destroyed." Jim said. "While we keep guard out here, our children will multiply in there. The other Zygons are frozen in their paintings, but not our kids. We stole technology the other Zygons would never have thought of. After four hundred years, there will be countless generations of our Zygon children in that painting who can take over this planet as their new home. They will fight the other Zygons and humans. They will be unstoppable."

"The painting has been moved around this country until it came here many years ago and was moved to the basement. A few weeks ago, they decided to put it on display." Michelle said. "People wanted to touch the painting and stare at it. If you look closely enough at it, you'll see our children. There used to be animals in this forest before our babies ate them. So, the people had to go."

"What happened to the people who disappeared?" Rory asked.

"We killed them." Tim said. "They were delicious."

"How are you planning on getting your children out of the painting?" Amy asked.

"Time energy." Jim said. "We used powerful Time Lord technology to get them in there. We need powerful time energy to get them out, but they're not ready yet. Time energy occurs naturally in those who have traveled through the time vortex. You say you know the Doctor. You must have traveled with him. You must have collected time energy we can use."

"We have lived for so long." Michelle said. "We need to find time energy now so we can use it later. I say we take theirs."

"An excellent idea my sister-in-law." Tim said.

Peggy, Amy, Rory, and Connie now knew what the Zygons wanted. However, it would not help them get out of this situation. The hungry Zygons prepared for their attack, staring at the agents and former time travelers with hungry eyes.


	8. The New SHIELD part 1

Chapter 8: The New S.H.I.E.L.D. part 1

The Iliad 2015

Agent Phil Coulson sat in his new office aboard the Iliad, a massive aircraft carrier sailing through the cold ocean, and was talking on the phone with former S.H.I.E.L.D. Director Nick Fury.

"You're welcome sir." Coulson said into the phone. "Im sure they can handle it. They're the Avengers."

Coulson then hung up the phone and hoped he was right about Earth's mightiest heroes. If they couldn't defeat Ultron, the world as mankind knows it would be lost forever. Suddenly, there was a slight wind inside the office followed by a loud wheezing sound. It was a sound Coulson recognized, but had not heard in over a year. Soon enough, the TARDIS started to form on the other side of the room. After it finished forming, the Doctor stepped out, followed by Clara Oswald and Jack Harkness. Coulson recognized Clara and Jack immediately, but the Doctor had since regenerated after Earth's dual invasion of Chitauri and Daleks when Coulson last saw him.

"Agent Coulson." The Doctor said. "I need your help."

"Who are you?" Coulson asked.

"What are you talking about?" The Doctor asked. "It's me. The Doctor."

"You certainly don't look like him." Coulson said.

"You had a different face last time we were at S.H.I.E.L.D." Clara whispered in the Doctor's ear.

"Clara? Jack?" Coulson asked.

"Yes." Clara said. "It's us. I promise. And this actually is the Doctor."

"How?" Coulson asked.

"Too complicated to explain." The Doctor said. "The short version is I got old."

"You're the same man who helped us stop the Chitauri and the Daleks?" Coulson asked.

"Yes." The Doctor said. "We've established that."

"If that's true, then you couldn't have come at a better time." Coulson said. "Tony Stark and Bruce Banner created an artificial intelligence called Ultron. From what Fury tells me, Ultron grew too powerful and took over Stark's Iron Legion."

"His iron what?" The Doctor asked.

"After the Chitauri-Dalek invasion," Jack said, "Tony Stark built hundreds of robot iron mans called the Iron Legion."

"And you've lost control of the machines." The Doctor said. "Typical."

"The Avengers are fighting Ultron and the Iron Legion in Novi Grad, Sokovia right now. I just got off the phone with Fury. I sent him the coordinates for a secret helicarrier that we're going to use to evacuate the people."

"Why would you use that to evacuate a town?" Clara asked.

"The town is flying." Coulson said. "Ultron did something that's making part of the city rise in the air. Eventually they're going to run out of breathable air. They could sure use your help over there Doctor."

"I want to help. I really do." The Doctor said. "But I came here seeking your help with another problem. Two criminal shape shifting aliens have stolen my friends' time energy and we don't know why. Time energy is powerful stuff. I need your help to find them and stop them before it's too late."

"With all due respect Doctor, if we don't help the Avengers, there won't be a world for any aliens to attack." Coulson said. "Even if I wanted to help you, I can't. My resources are limited."

"Aren't you the Director of S.H.I.E.L.D.?" The Doctor asked.

"I'm a Director of S.H.I.E.L.D." Coulson replied. "I've been trying to rebuild S.H.I.E.L.D. after the H.Y.D.R.A. infiltration. Then we found out that there was another S.H.I.E.L.D. that believed I wasn't doing a great job and that wanted to take me out. We're on their boat right now."

"This is an office." Jack said. "Not a prison."

"I've been negotiating with them." Coulson said. "I'm trying to get them to allow me to be the Director and for the high ranking members of this new S.H.I.E.L.D. to be my council. I hope everyone can get behind that."

"You still have your team right?" Clara asked.

"Not exactly." Coulson said. "Ward's a traitor. He was working for H.Y.D.R.A. the whole time. Fitz and Simmons aren't working well together like they used to and May's mad at me for a few reasons. She was recruited by the other S.H.I.E.L.D. too. I've had some new members since we last met. One of them, Agent Triplett, died while we were in Puerto Rico. Then there were two other agents Bobbi Morse and Mack, who were working for the other S.H.I.E.L.D. and never had any loyalty to me. Then there's Morse's former husband Lance Hunter, who started out as just a mercenary."

"What about Skye?" The Doctor asked.

"That's complicated." Coulson said.

"I've seen my fair share of complicated." The Doctor said.

"Alright." Coulson said. "Skye became inhuman."

"What's inhuman?" Clara asked.

"It's a designation for people with extraordinary abilities." Coulson said.

"How did she become this way?" The Doctor asked.

"Now that would take awhile to explain." Coulson said. "Let me just tell you where Skye is now. She's here. At first she was taken by a man with no eyes somewhere she could learn to control her powers. Then she and one of her inhuman friends came back. I think his name is Lincoln. After a misunderstanding, Lincoln ended up hurt, badly. He's here in the ship's sick bay recovering. Skye is staying with him."

Suddenly, Jack's cell phone started to ring. He picked it up and saw that Gwen Cooper, the only other surviving member of Torchwood, was calling him.

"This is important." Jack said. "Gwen might've found something about the Zygons."

"The what?" Coulson asked.

"The shape shifting aliens we told you about." The Doctor said.

Jack answered the phone and let Gwen explain what she found to him. After a few minutes, Jack hung up.

"We have a problem." Jack said.

"What?" The Doctor asked.

"Gwen said that two men were found dead at a train station in London with their luggage." Jack said.

"What does that have to do with the Zygons?" The Doctor asked.

"The two men were waiting for a taxi to take them to Heathrow Airport." Jack said. "They bought plane tickets to Moscow. They were found with their tickets and passports missing. An hour later, there is footage of those same two men at the airport in Heathrow. Gwen's at the airport now trying to find them, but it's hard to find something that keeps changing form. Do you see the problem now?"

"I'm afraid I do." The Doctor said. "The Zygons are taking the shape of those men so they can get on a plane to Moscow and attract little suspicion."

"Why are they going to Russia with time energy?" Clara asked.

"I don't know." The Doctor said. "Do you see why we need S.H.I.E.L.D.'s help Coulson?"

"Need our help?" Coulson said. "We need your help. Ultron is going to destroy the planet if we don't help the Avengers."

"So what do we do?" Clara asked.

"We'll just have to figure something out." The Doctor said.

* * *

3W Institute 2015

Inside her bright white office, a woman in a purple coat and dress watched the Doctor and Coulson on her computer screen. Her name was Missy.

"Oh Doctor. Whatever will you do?" Missy said and then started chuckling. "The time is coming Doctor. You need to make a decision before it's too late."


	9. The Bad Wolf part 1

Chapter 9: The Bad Wolf part 1

Moscow, Soviet Union 1946

Agent Carter, Amy Pond, Rory Williams, and Connie Oswald had just discovered the Zygons' plans. However, they were trapped in a long hallway of a Russian art museum with one Zygon standing on one end and the other two Zygons standing at the other. The Zygons could not let these four intruders escape with the knowledge of their plans. The only solution was to kill them. However, just as all hope seemed lost, there was a slight breeze in the hall, which seemed weird because there were no open doors or windows. Then, they all heard a loud, wheezing sound. Amy and Rory recognized it immediately as the sound of the TARDIS. They hadn't heard it in so long. The two of them gave up hope a long time ago that they would ever hear it again. After all this time, they were finally about to be reunited with the Doctor. The Zygons had only heard rumors about the Doctor, but they knew what he was capable of. They would need to destroy him as well. The TARDIS materialized next to the wall, with the Zygon painting in the back of the TARDIS and Amy, Rory, Peggy, and Connie merely a yard from the TARDIS doors. Soon, the doors opened and the Doctor stepped out. However, this was not the Doctor who had traveled with Amy and Rory. This Doctor had a different face. He was either from the past and would have no idea who they were, or he was from the future and would be happy to see them. They had traveled with the eleventh Doctor and this man was the tenth.

"Hello." The Doctor said. "I heard there was a painting that went up here a few weeks ago. Then a bunch of people started disappearing. Do you know anything about that?"

"Doctor." Amy said. "It's the Zygons."

The Doctor looked to the left and right, at both ends of the hallway, and saw Zygons.

"Doctor, what is it?" Rose Tyler asked as she too stepped out of the TARDIS.

"Who's blondie?" Amy whispered to Rory.

"How should I know?" Rory whispered back. "He doesn't seem to recognize us. This must be the Doctor before we met him."

"Are you the Doctor?" Peggy asked.

"Yes." He replied. "Who are you and how do you know about me?"

"I'm Agent Peggy Carter." She replied. "This is my assistant Connie."

"Hello." Connie said.

"I've read many of your records." Peggy said. "I've also heard much about you from Amy and Rory."

The Doctor now looked at Amy and Rory, wondering who they were.

"If you're quite finished." Tim the Zygon said. "You've arrived just in time Doctor. We were about to kill your friends. Now we can kill you too."

Rose stepped forward and noticed a painting on the wall next to the TARDIS. Ignoring the Zygons, she called the Doctor to look at it. They both looked at the painting and smiled at each other. Curious, Amy walked over to look at it as well. There was nothing special about this painting. It was white with some Russian letters spelled out in red. She couldn't even read it. Suddenly, she could feel the TARDIS entering her brain, something she hadn't felt in a long time. Then, the Russian letters became English and she could read them. The words read "Bad Wolf".

"What's Bad Wolf?" Amy asked.

"What is so important that it distracts you from us?" Jim the Zygon asked.

"Ever heard of the Bad Wolf?" The Doctor asked the Zygons.

"Of course we have." Michelle the Zygon said. "Legends of its power are known throughout the universe."

"It's me." Rose said. "I'm the Bad Wolf."

"You're just a human girl." Tim said.

"A human girl who killed the Dalek Emperor." Rose said.

"Emperor?" Amy and Rory thought to themselves. They remembered the Daleks having a parliament.

"It matters not." Jim the Zygon said. "We're still going to kill you."

The three Zygons then let out a massive roar and started running towards the center of the hallway where all the humans were.

"I was really hoping that would intimidate them." Rose said.

"What do we do!" Connie yelled. Noting that the Zygons were getting closer at a rapid pace.

Equally rapidly, the Doctor whipped out his sonic screwdriver and held it high above his head. Then, he activated the device, creating a sonic noise that pierced the Zygon's ears and made them scream, stop running, and fall to the ground, momentarily paralyzed. The Doctor and the humans were unaffected.

"Run!" The Time Lord yelled.

The Doctor, Rose, Peggy, Connie, Amy, and Rory then ran out past the Zygons and out of the hallway, leaving the TARDIS behind. The Zygons would only stay down for a few moments before they would begin hunting down the intruders. The Doctor and his new group ran back through the museum towards the entrance. Once they reached the front doors, they stopped to catch their breath before going back outside on this cold, Russian night.

"Amy and Rory is it?" The Doctor asked.

"Yes," They both replied, still out of breath. There was a time when they were used to running with the Doctor, but that was a long time ago and they needed more time to readjust,

"How is it you know so much about me?" The Doctor asked.

"I'm not going to lie to you Doctor." Amy said. "Rory and I are from your future and that's all I'm going to say about it. Can't risk messing up time."

"I see." The Doctor asked.

"Do you know me?" Rose asked. "Where am I in the future?"

"Who are you?" Amy asked. "The Bad Wolf?"

Rose suddenly grew silent. This woman was from the Doctor's future, but had no idea who she was. Rose wondered where she would be by the time the Doctor met them.

"That's enough of that." The Doctor said. "This is Rose. Why are you all here?"

"Same reason as you." Peggy said. "We were investigating the disappearances here."

"And it's the Zygons." The Doctor said.

"What are Zygons exactly?" Rose asked.

"Alien shape shifters." The Doctor said. "But I have no idea what they're doing here."

"We do." Connie said. "They told us their plan."

"What is it?" The Doctor asked.

The group suddenly heard the roars of the angry Zygons swiftly approaching them.

"We'll tell you later." Peggy said. "We need to get out of here, now."

The six of them rushed out the door and started running away from the museum. Suddenly, as they ran onto the sidewalk, Amy caught sight of something horrible a few yards in front of them.

"Stop!" Amy yelled.

This particular city street was deserted at this time of night. However, Amy noticed an evil figured standing before them down the street. Rory and the Doctor soon recognized it as well.

"What is that doing here?" Rory asked.

"I don't understand." Peggy said. "It's just a statue."

"It's a statue when you see it." The Doctor said.

The figure before them was a Weeping Angel, and it looked hungry.

"What about when we're not looking at it?" Connie asked.

"It will kill you." Amy said.

"Just don't blink." The Doctor said.

"Doctor!" Jim the Zygon yelled.

The group turned around to see the three Zygons, (Tim, his brother Jim, and Jim's wife Michelle) standing at the other end of the street. Amy realized that no one was looking at the Angel and turned around. It had moved to be simply two feet away from the group now. Amy was once again face to face with her biggest fear.


	10. The New SHIELD part 2

Chapter 10: The New S.H.I.E.L.D. part 2

The Illiad 2015

Agent Coulson, The Doctor, Clara Oswald, and Jack Harkness stood in Coulson's office aboard the Illiad and contemplated what to do. At this very moment in London, two criminal Zygons were trying to board a plane to Moscow with stolen time energy to do something with catastrophic consequences to the Earth. No one here knew what their plans were exactly. At the same time, Ultron and his Iron Legion were attacking Novi Grad, Sokovia. He had done something that elevated much of the city so that it flew upwards. Once it reached optimal height, Ultron planned to drop it and create an explosion large enough to wipe out most of the human race. The Avengers were already fighting in Sokovia and Coulson knew that they could benefit from the Doctor's help somehow. However, there would be severe consequences if they neglected the Zygon problem completely. Coulson wanted to divide his forces, but he didn't have much authority anymore, even over his own team. May was mad at him for keeping secrets. Skye's loyalty is not clear, as she is heavily invested in both the Inhumans at the Afterlife sanctuary with her mother Jiaying, and S.H.I.E.L.D. Bobbi Morse and Mack were never really working for him and Bobbi has always had a strong hold over her former husband Lance Hunter. That meant that the only agents at his disposal who might actually help him were Leo Fitz and Jemma Simmons, a pair that has been struggling to be friends for the better part of this year. Coulson took out his cell phone and texted Fitz and Simmons separately, telling them to report to his office.

"Who are you texting?" The Doctor asked.

"There's only two agents on this whole boat who might actually help us." Coulson said. "Fitz and Simmons. I've just asked them to come here."

The Doctor, Clara, and Jack were very happy with this news. Fitz had accidentally traveled with the Doctor and Jack. While they were trying to get back to Earth to stop the Dalek-Chitauri Invasion, they ended up traveling through time and space fighting the Juddoon, looking for Thor's hammer, and discovering a Dalek base on the moon. Clara was left behind on Earth and became great friends with Simmons, being the only English girls (except for Martha Jones) in the midst of American heroes and agents. They traveled the world together looking for the Avengers and fighting aliens. They went to Brazil, California, Canada, London, Australia, and even the Dalek Command Ship in space. She would be happy to see her friend again.

"That's good." The Doctor said. "I've missed old Fitz."

"I should warn you." Coulson said. "He's not the same as when you last saw him."

"How so?" Jack asked.

"After Ward betrayed us he tried to kill Fitz and Simmons." Coulson said. "It's a long story, but the short version is that they survived, but Fitz had a brain injury. He's been slowly recovering ever since. At this point he's actually mostly like his old self again."

"So what are they going to do?" The Doctor asked. "What is your plan?"

"We divide up our forces." Coulson said. "I'm thinking you'll drop off whoever you'd like at the airport in London and then continue on to Sokovia to assist the Avengers. I wish I could come with you, but I have to try and manage things here. S.H.I.E.L.D. could collapse on itself if I'm not here. That's the last thing we need if we're going to fight Ultron and these Zygons."

Then, Fitz and Simmons walked into the room. They were overjoyed to see the TARDIS and their old friends Clara and Jack. However, they were confused by the strange old man.

"Clara!" Jemma said. "What are you doing here?"

"We came to ask your help." Clara said.

"Where's the Doctor?" Fitz asked.

"I'm right here." The Doctor said, again forgetting that he's since regenerated from the last time he saw Fitz.

"How can you be him?" Fitz asked. "Did you age really fast?"

"Something like that." The Doctor said.

"It is him." Jack said. "This isn't the first time he's changed appearances."

"Prove it." Fitz said.

"Ok." The Doctor said. "You and I met in an underground tunnel in New York City being chased by a Cyberman. Then, we stopped a Weeping Angel and discovered a plot by the Daleks to kill the Avengers. On our way back to S.H.I.E.L.D. headquarters in Washington DC, our plane was invaded by Krillitanes who sent the TARDIS away. We ended up in Victorian England where you and Skye were kidnapped by Juddoon because they thought one of you was Captain Jack Harkness. Then we rescued you, or rather River Song did. Then we ended up on Asgard where Thor asked us to find his hammer, which was hard because it was on another planet and in the future. We took it from a Frost Giant, discovered a Dalek base on the moon, and came back to Earth at the S.H.I.E.L.D. base in Sydney, Australia."

"Alright I guess it is you." Fitz said. "What do you want us to do?"

"There are shape shifting aliens in London with stolen time energy trying to get to Moscow by plane." The Doctor said.

"The Avengers are also dealing with a crisis in Sokovia." Coulson said. "I want you to join the Doctor's team to help them fight both problems."

"What about here?" Jemma asked. "What about the Inhumans?"

"I'll still be here to manage that." Coulson said. "Will you help them?"

"Of course." Fitz said.

"Count me in too." Simmons said.

"Great." The Doctor said. "Former Torchwood agent Gwen Cooper is already in London. I'll bring one of you and Jack there. The rest will come with me to Sokovia. I'll pick up the team in London when we've finished with the Avengers."

"I'll go with you to London." Jemma said. "It's been awhile since I've seen England."

"Thank you for your help agent Coulson." Clara said.

"I'm sorry I couldn't be more help." Coulson relied.

"Alright." The Doctor said. "Everyone in the TARDIS. There's no time to lose."

Clara, Jack, Fitz, and Simmons obeyed the Doctor and rushed into the TARDIS. Fitz and Simmons did not forget how truly amazing it was inside the blue box. The Doctor said goodbye to Coulson before boarding the TARDIS. Coulson then watched as the Time Lord's time machine faded away on its way to London, again.

* * *

3W Institute 2015

Missy continued to watch the Doctor on her computer screen in her office.

"Now don't hurt Ultron too badly." Missy said. "He plans on killing a lot of people, which is the only way I'll get enough Cybermen."

Missy then gave a villainous grin as she waited to see what would happen when the Doctor arrived in Sokovia.


	11. The Bad Wolf part 2

Chapter 11: The Bad Wolf part 2

Moscow, Soviet Union 1946

It was midnight in the city. Agent Carter, Amy Pond, Rory Williams, and Connie Oswald had broken into an art museum here to investigate aliens and they found Zygons. They discovered that these Zygons were criminals. They were hiding their family members in Russian paintings until the twenty first century, when they would come out and do battle with the good Zygons in English paintings since 1562 and try to conquer the planet. The tenth Doctor and Rose Tyler soon arrived, planning to investigate the same thing. They joined the four others and ran out into the streets to avoid the three Zygons (Tim, his brother Jim, and Jim's wife Michelle). However, on the quiet street they had run onto (no police or civilians to be found), there was a Weeping Angel which had moved to just two feet in front of them. Amy stared at it, knowing what would happen if she let it touch her. The rest of the group looked behind them at the three Zygons who had followed them onto the deserted sidewalk. The Zygons stood far away at the other end.

"What is the Bad Wolf going to do now?" Jim asked sarcastically. "Even she can't stop us."

"You know we can't let you leave here alive." Tim said.

"Doctor!" Amy shouted. "More people need to watch the Angel. I can't not blink forever."

Peggy and Rose turned around to assist Amy in stopping the Angel from moving, while the Doctor, Rory, and Connie continued to watch the three Zygons far at the other side of the sidewalk.

"I've got a plan for that." The Doctor said to Amy as he whipped out his sonic screwdriver and fidgeted around with it.

"What are you doing?" Tim asked.

"Getting rid of your Angel." The Doctor said.

"Our what?" Jim asked.

"You can't tell because we're all standing here, but there's a Weeping Angel behind us. I assume you sent it after us." The Doctor said.

"We did no such thing." Michelle said.

"They're not working with the Angel." Rory said. "So what's it doing here?"

"It must be a scavenger." The Doctor said. "It's probably all alone and came here looking for food."

"So what's the plan for the Angel?" Connie asked.

"I am very good at teleports." The Doctor said. "I just have to set the frequency right."

"Enough of this!" Michelle yelled.

Michelle then started to charge at the six of them.

"Let's go." Tim said.

"No." Jim said. "Let my wife have this one. She hasn't had a hunt in ten years."

So, the other two Zygons let Michelle run at the Doctor and his friends alone.

"What's happening?" Rose asked. She could not see as her eyes were fixed on the Angel.

"Doctor?" Agent Carter asked.

"One second." The Doctor said.

The Doctor then raised his sonic screwdriver into the air and pressed the button. Then, a blue light started to consume the angel and Michelle entirely and after a few moments the lights had faded away, taking the Angel and the Zygon with them. The Doctor had teleported them somewhere else. Amy, Rose, and Peggy felt like they could finally blink safely now that the Angel was gone.

"Where did you send them?" Connie asked.

"Where is my wife!" Jim screamed.

"I was trying to teleport the Angel to the center of the sun." The Doctor said. "Your wife was accidentally transported there as well."

"No!" Jim screamed. "She's dead!"

In a flash of extreme anger, Jim charged at the Doctor and his friends. Tim stood back and watched, letting his brother have his own revenge. Jim was approaching them much faster than Michelle was. The Doctor was having difficulty fidgeting with his screwdriver in time to send Jim away. Realizing that the Doctor would not be finished in time to save them, Connie Oswald ran forward towards the Zygon. She was going to sacrifice herself. She and Jim met halfway, where Jim threw her to the ground and bit into her stomach, trying to eat her. Connie's blood started to pour onto the sidewalk.

"No!" Peggy screamed.

Just then, the Doctor had finished adjusting the screwdriver. Then, he activated the device, just as he had done in the museum, creating a sonic noise that pierced the Zygon's ears. Tim fell to the ground in pain. Jim ran away from Connie's body to join his brother. The Doctor then stopped pressing the button and began recalibrating the device once more.

Peggy Carter ran towards Connie to be with her dying friend in her final moments. Her wounds from the Zygon were too severe to be treated. Amy, Rory, and Rose watched as Connie whispered something in Peggy's ear. They then watched the Zygons. They were not getting up, even though the noise had stopped. This time, the Doctor had made the sonic noise lethal. The two Zygons were now very weak. After he finished his calibrations, the Doctor pressed the button one more time. Then, he, Rose, Amy, Rory, and Peggy were consumed by a bright blue light and disappeared from the street. They reappeared back inside the museum where the TARDIS had landed.

"I'm so sorry." The Doctor said to Peggy.

"What did she whisper to you?" Rory asked.

"It was a message for the Doctor." Peggy said.

"What was it?" The Doctor said.

"She said, run you clever boy," Peggy said, "and remember."

"Remember what?" The Doctor asked.

"I have no idea." Peggy said.

"Where do you all live?" The Doctor asked.

"New York City." Amy said.

"Well then hop inside the TARDIS and I'll take you back there. The Zygons should be dying. There's no point in us staying around here and killing them. I'll let them die on their own." The Doctor said.

Then, everyone piled into the TARDIS. Soon, the blue box faded away from the Soviet Union.

* * *

Amy and Rory were fascinated to see how the TARDIS looked before they met the Doctor. It looked similar to how they remembered it, with only a few differences. Agent Carter was happy to finally have the chance to see the inside of the TARDIS firsthand. However, even this could not distract her from the recent loss of her dear friend Connie. The TARDIS returned to Manhattan next to the Empire State Building. It was midnight in Russia where they last were, so the Doctor brought them to New York at midnight so that it would be easier for them to adjust to time zones. Peggy said goodbye to the Doctor and walked outside. Amy and Rory knew this would be the very last time they would be in the TARDIS. In the future, this machine would take them to far away worlds and time periods. It was the adventure of a lifetime and leaving the TARDIS now was like admitting to themselves that it was finally over.

"Thank you for all your help." Amy said.

"It was my pleasure." The Doctor said.

"I doubt we'll be seeing you any time soon." Rory said. "At some point though, you'll be seeing a lot of us."

"What about me?" Rose asked.

"Spoilers." Amy said. She had no idea why Rose wasn't around when they met the Doctor. Saying spoilers is something Amy had picked up from her daughter, River Song, and it usually worked in ending conversations about the future.

Amy and Rory took one last good look at the TARDIS interior and then walked outside.

"I'm nervous." Rose said to the Doctor. "Something's going to happen to us. That's why they don't know me in the future. Something terrible is going to happen."

"Relax Rose." The Doctor said. "The future isn't guaranteed. Besides, you're the Bad Wolf remember?"

Rose smiled at him.

* * *

New York City, United States 1946

Peggy, Amy, and Rory watched as the TARDIS faded away from New York.

"We never told the Doctor what the Zygons were planning." Amy said.

"He thinks it won't matter." Peggy said. "If those Zygons die now, they won't be around in the twenty first century. Everything should work out fine."

"I have a feeling that it won't." Rory said. "What if they survive?"

"You should go back to your apartment and get some rest." Peggy said. "There's some people I have to talk to about Connie."


	12. The Torchwood Team

Chapter 12: The Torchwood Team

Heathrow Airport, London, England 2015

The TARDIS materialized in a women's restroom at Heathrow Airport in London. Fortunately, Gwen Cooper happened to be in here washing her hands and was the only woman there. Jack Harkness and Agent Jemma Simmons soon stepped out of the TARDIS. Jack, seeing his old friend Gwen, ran over to her and the two embraced in a hug. Then, they turned around and watched as the TARDIS, carrying the Doctor, Clara Oswald, and Agent Fitz, faded away on its way to Sokovia to assist the Avengers in defeating Ultron.

"It's so good to see you again." Gwen said to Jack.

"How are Rhys and the baby?" Jack asked.

"Good." Gwen replied. "We're all having a holiday here in London. I wasn't going to let them come with me here to hunt for alien Zygons."

"Hello." Jemma said as she stepped forward. "I'm Agent Jemma Simmons. I'm with S.H.I.E.L.D."

"You seem a bit young." Gwen said. "You didn't tell you you were with S.H.I.E.L.D. Jack."

"I joined last year after the Dalek-Chitauri Invasion." Jack said. "Then that whole business with H.Y.D.R.A. came up and I had to lay low in London with Martha and Mickey."

"You both know each other from Torchwood, right?" Simons asked.

"Did you tell S.H.I.E.L.D. everything about our top secret alien organization?" Gwen asked Jack.

"Jack didn't tell me anything." Jemma said. "I was hacking government computers since before high school. I found out about Torchwood a long time ago. It's a shame it was shut down."

"I like her." Gwen said to Jack.

"So tell me about the Zygons." Simmons said.

"The next plane to Moscow leaves in ten minutes." Gwen said. "We have to stop them from boarding the plane."

"This airport is massive. How are we supposed to get to the gate in time?" Simmons asked.

"It's right outside this bathroom." Gwen said.

"The Zygons stole time energy from me, Martha, and Mickey." Jack said. "Now they're going to take it to Russia. We have no idea why, but we don't want to find out."

"They're disguised as two men wearing bright green coats. You can't miss them." Gwen said. "They have stolen passports and everything. The only people who know they're even here are us three. So it's up to us."

"Just like old times." Jack said. "It's like we're doing a mission for Torchwood again. What do you say Simmons? Want to join the old Torchwood team on this one?"

"Absolutely." Simmons said. "We should get moving if we've only got ten minutes."

The three of them then walked out of the ladies' room and saw a large window in front of them. Outside the window was the plane destined for Moscow. Below, Jack, Gwen, and Jemma saw luggage and boxes being loaded onto the plane's cargo hold through a conveyer belt. Then, they turned to the right. Across the small hallway, they could see passengers showing their identification and tickets to board the airplane. Then, they saw two men wearing bright green coats. One was carrying a small suitcase. Jack assumed that the orb containing the stolen time energy was in there.

"That's them." Gwen said.

The men were about to give the airline woman their tickets and board the plane if the impromptu Torchwood team did nothing. So, Jack reached into his pocket and pulled out a laser gun that he took from the TARDIS' armory on the way to London. Jemma pulled out the same kind of laser gun from her own pocket.

"What are you planning?" Simmons whispered to Jack.

"Freeze Zygons!" Jack yelled as he pointed the gun at the two men in green coats. Everyone in the area grew silent as they stared, confused and scared, at Jack, Simmons, and Gwen.

"Do you even think before you do something stupid?" Gwen asked.

"Jim and Tim." Jack said. "The boys in the green coats. I'm talking to you."

Everyone's eyes were so fixed on Jack, that they didn't realize that the two men in green coats had started to change. Their bodies were morphing and transforming. As shape shifters, the Zygins were masters of deception. Soon, the two men had transformed into beautiful young air stewardesses. Just then, airport security arrived next to the passenger line.

"Those three are terrorists!" Jim the Zygon (disguised as an air stewardess) said to the police.

The police then started to advance towards the Torchwood team. As they did, the two air stewardesses walked right through the gate and boarded the plane to Moscow.

"We can't shoot them." Simmons said. "This is all just a misunderstanding."

Gwen then grabbed the gun out of Jemma's hand, aimed it at the ceiling, and fired a powerful laser blast. Chunks of the ceiling began to fall, forcing security to back off and dodge them. Gwen then turned and fired a blast at the glass window, shattering it.

"Go." Gwen said to Jack and Simmons. "Get on that plane. I'll keep them busy here."

"What if they catch you?" Jack asked.

"I can take care of myself Jack. You know I can." Gwen said. "Now run!"

By now, the chunks of ceiling had finished falling and airport security was preparing to fire at the trio. So, Gwen fired first. The police and civilians took shelter behind their seats and in the bathroom. Jack and Simmons then ran over to the window and jumped through it. They had fallen about two stories to the ground with only minimal damage to their bodies. The men loading the plane's cargo were so distracted by the fighting going on with Gwen in the terminal, that they did not notice as Jack and Jemma jumped onto the conveyer belt and were lifted into the plane's luggage ad cargo hold. Jack and Jemma then hid behind boxes and suitcases.

"Is Gwen going to be alright?" Simmons asked.

"I hope so." Jack said. "Some Torchwood reunion this turned out to be."

When Gwen saw that Jack and Jemma had boarded the plane, she stopped firing. After all, she did have the potential to kill innocent people. She then let airport security arrest her and she was taken away for questioning. All Gwen had to do was say the word "Torchwood" to them and the police would essentially back off and let her go. It had worked many times before and it would work again now. Ten minutes later, the plane took off from Heathrow Airport and was flying through the skies of England on its way to Moscow, Russia. Jack then took out his wrist communicator and contacted the Doctor.

"Doctor." He said. "This is Jack. We couldn't stop the Zygons in London. They got on the plane, but we got on with them. We'll get them when we land in Russia. How are things in Sokovia."

"Call back later Jack." The Doctor said. "Ultron is really doing a number on this city. It's literally flying in the air. I don't know how high it can go."

"Are the Avengers there?" Jack asked.

"Yes." The Doctor said. "I'm really busy over here Jack. Call back later."

The Doctor then hung up on Jack.

"Sounds like they could really use our help." Simmons said.

"Just focus on this." Jack said. "Defeating Ultron means nothing if we don't also stop these Zygons."

* * *

3W Institute 2015

Missy watched the battle in Sokovia on her computer screen in her office. She saw the Doctor, Clara, and Fitz there as well.

"Now don't go and die on me Doctor." Missy said. "Then everything I did would be for nothing."

Suddenly, Missy's door opened and in walked Seb, her assistant.

"Hello." Seb said.

"What is it?" Missy said. "I'm trying to watch the show."

"Hundreds more people have started arriving every hour." Seb said. "We're having a little trouble processing it all."

"It's from Sokovia." Missy said. "So many people there are dying. I don't care if it's a lot. Get on top of it. My army will rise very soon and they all better be ready when that happens."


	13. Jiaying

Chapter 13: Jiaying

New York City, United States 1946

It was seven o'clock in the morning. Amy and Rory were moving about their apartment preparing for another work day. It had been a week since their adventure in Moscow with Agent Peggy Carter, Connie Oswald, the tenth Doctor, Rose Tyler, and the Zygons. Connie was killed and the Zygons were presumed dead. Now, they had to accept that their adventuring days were over and that it was time to live a normal life, which they were also content with. Rory was now an official doctor at a hospital downtown and Amy was still looking for a job at the current moment. Suddenly, they heard a knock on the door.

"Who could that be at 7:00 a.m.?" Rory asked.

Amy walked over to the door and opened it to find Agent Peggy Carter on the other side.

"Peggy!" Amy said with a smile. "It's so good to see you. Come in."

Peggy walked inside and went into the living room with Amy and Rory.

"I have some news." Peggy said. "The Zygon painting that was on display at that art museum in Russia has been taken down and relocated to the basement of the museum in storage. The museum has since reopened with no problems."

"The Doctor was right." Amy said. "The Zygons will eventually just die off. They may even be dead right now."

"I still just can't shake the feeling that this isn't over." Peggy said. "Maybe I'm still sad about Connie. I fear I'll be leaving New York soon. Probably some time in the next few weeks. I don't want to leave you both. Who else can I talk to about all this?"

"We're happy to talk with you any time." Rory said.

"If you ever need help with aliens again, give us a call." Amy said. "Rory and I do know a thing or two about aliens."

Agent Carter smiled and hugged them.

* * *

Moscow, Soviet Union 1966

Jim the Zygon walked the halls of the Russian art museum where the painting that contained his species was housed in storage. Jim was currently disguised as a security guard. It was night and the museum was closed. He was just making his usual rounds to make sure no one got in at night and threatened the painting. Twenty years ago, his wife was killed by the Doctor, leaving only Jim and his brother Tim to guard the painting until human society was advanced enough for their criminal Zygon family to be released from the painting. Then, the criminal Zygon family would take over the planet. However, the good Zygons were hidden away in different paintings in London with largely the same mission. Jim wanted the new Earth to be one made by the criminal Zygons. As a smart alien, he knew that Earth technology might advance to the point where they could stop his plans. So, he came up with a plan B just in case. He had gathered together a second army, which no humans could control because this second army was inhuman. Jim was wearing a wrist communicator. He held it up to his face and spoke into it.

"Tell me your progress on plan B." Jim said.

* * *

Afterlife 1966

Jiaying walked down the outside path of her community of inhumans on a cloudy day. It looked as though it would rain later. She'd spent much of her time creating this place and recruiting inhumans, people with superhuman abilities, to teach them how to control their powers and use them effectively. Jiaying was wearing a wrist communicator and heard it beep. She held it up to her face and pressed a button.

"Tell me your progress on plan B." Jim the Zygon said from Russia.

"It's slow right now." Jiaying said. "The inhumans that I have now are growing stronger, but there still aren't enough of them. Have you made any progress in finding time energy to get the others out of the paintings?"

"Not yet, but we will continue to hunt the Doctor and his companions until we get what we need." Jim said. "However, in case we fail, I need to know that what you're doing at Afterlife will benefit us."

"It will." Jiaying said. "I've told all these humans that I'm helping them unlock their potential. They don't know that I'm turning them into weapons. They're so gullible."

"Humans." Jim said with a chuckle. "They're so stupid."

"I couldn't have said it better myself." Jiaying said. "Keep looking for the Doctor and I will keep up my efforts here. We will rise again one day."

* * *

3W Institute

Connie awoke suddenly. It was like waking up from a nightmare. Her heart was pounding. The last thing she remembered with being killed by a Zygon in Moscow. Had it all been a dream? Connie now found herself sitting in an office. The room was entirely white and there were no windows. Suddenly, the door to the office opened and in walked Missy.

"Hello dear." Missy said. "How are you?"

"Where am I?" Connie asked.

"You're in my domain now." Missy said. "You'll need to be converted soon, but I decided to pop in and see you. I like to check up on all of Clara's echoes when they die."

"Who's Clara?" Connie asked.

"She's sort of like your mother in a manner of speaking." Missy said.

"I already have a mother." Connie said. "Her name was Susan. She died when I was young."

"Yes I know." Missy said. "She died and then she came here just like everyone else. Now she's one of mine."

"One of your what?" Connie asked.

"One of my Cybermen." Missy said with a villainous grin.


	14. The Battle of Sokovia

Chapter 14: The Battle of Sokovia

Novi Grad, Sokovia 2015

The TARDIS materialized on a street corner near the edge of the city, which was now rising high into the air. The Doctor, Clara, and Fitz ran outside and were shocked by the scene around them. Much of the city's buildings and infrastructure had been destroyed. Rubble and fire were all that could be seen on the ground. The air was polluted with smoke and debris. Ultron's robot minions were also flying through the air. People ran for their lives through the broken streets. The Doctor, Clara, and Fitz noticed that they all seemed to be running in one direction. They followed the crowd to the very edge of the town. They could tell by the way the sky was moving that the city was still ascending. They also saw Coulson's giant S.H.I.E.L.D. helicarrier parked in the sky near the town. On the edge, Captain America and Black Widow were working to get civilians onto air shuttles that would transport them to the safety of the helicarrier. Two more new avengers, Scarlet Witch and Falcon, were also helping, though the Doctor didn't recognize them. The Doctor was horrified by the destruction around him. He could see why Coulson wanted him to come here and help. The Zygon threat seemed like nothing compared to this. However, the Doctor knew that when the Zygon plan was complete, the destruction could be even worse than what he was seeing now. He was wearing a wrist communicator, so that he could keep in touch with Jack Harkness and Agent Simmons in London. The communicator started to beep. Jack had a message.

"Doctor." He said. "This is Jack. We couldn't stop the Zygons in London. They got on the plane, but we got on with them. We'll get them when we land in Russia. How are things in Sokovia."

"Call back later Jack." The Doctor said. "Ultron is really doing a number on this city. It's literally flying in the air. I don't know how high it can go."

"Are the Avengers there?" Jack asked.

"Yes." The Doctor said. "I'm really busy over here Jack. Call back later."

The Doctor then hung up on Jack.

"What do we do?" Fitz asked.

The Doctor didn't answer. Instead he ran towards Captain America so that they could discuss how best to assist. The Doctor reached the Captain as he was guiding civilians into air shuttles. Clara and Fitz trailed behind.

"Hello again." The Doctor said. "How can I help?"

"Please proceed to the shuttles sir." Captain America said. "We'll get you out of here safely."

The Doctor was momentarily confused by the Captain's response until he remembered that he had regenerated since last seeing him. Clara and Fitz then arrived.

"Doctor." Clara said. "You can't just run off like that."

"Clara? Fitz?" The Captain said. "What are you doing here? Where's the Doctor?"

"This wrinkly old man is the Doctor." Clara said. "He's the same man who helped us stop the Dalek-Chitauri Invasion."

"So I'll repeat." The Doctor said. "How can I help?"

While Captain America was puzzled, he didn't have time to question it. Soon, Black Widow ran over when she caught sight of Clara and Fitz talking to Steve. They explained to her as well that the Doctor had regenerated. Falcon and Scarlet Witch, curious about what was happening that would make Captain America and Black Widow stop working, also came over. These two new Avengers were helping in the fight. Falcon, aka Sam Wilson, used his wings to fly around and help people as well as shoot at Ultron's robots. Scarlet Witch, aka Wanda Maximoff, was using her psychic powers and telekinesis to help. Natasha introduced them to the Doctor. There were other new additions to the team as well that were fighting in other sections of the city, including Vision (a powerful artificially constricted man using the power of the Mind Stone), War Machine (a friend of Tony Stark who uses a similar Iron Man suit), and Quicksilver (Wanda's brother with the power of super speed). The Avengers told the entire story of Ultron to the Doctor. The Time Lord then told the Avengers all about the Zygons, but they all agreed that this business here in Sokovia was more important at the present moment. The Avengers then received a message from Tony Stark and Thor, who were fighting with Hulk and Hawkeye in other parts of the city, saying that they needed urgent help. The four Avengers then left to help their comrades, leaving the Doctor, Clara, and Fitz to stay and help guide people onto the shuttles.

"I wonder what P.E. will have to say about this." The Doctor said.

"Who's P.E.?" Fitz asked.

"Clara's boyfriend." The Doctor said.

"His name is Danny." Clara said. "He's probably watching this on the news. He's actually in Moscow today for his friend's bachelor party."

Clara suddenly remembered that there were Zygons trying desperately to get to Moscow.

"Aren't the Zygons going there on a plane right now?" Fitz asked.

"I need to warn him!" Clara said.

"Focus on not getting killed right now." The Doctor said. "When this is over, I'm hoping the Avengers will help us."

"We'll help too." Fitz said. "I don't mean just me and Jemma. I mean the old S.H.I.E.L.D. team. May and Skye will happily help us. I know they will."

"Coulson doesn't think so." The Doctor said.

"He's got a lot on his mind." Fitz said. "We've all been through a lot recently, but I know they'll help."

"That's good to know." The Doctor said.

* * *

The Battle of Sokovia raged on for about another hour. The Doctor, Clara, and Fitz were able to successfully assist in getting civilians onto the helicarrier and then transporting themselves to the helicarrier inside the TARDIS. The Doctor refused to leave his beautiful time machine in a floating, crumbling, war zone. The Avengers were able to destroy Ultron and get out of the city before it exploded in the sky, an explosion that would have caused an extinction event if it had hit the ground. Unfortunately, Quicksilver was killed in action. After the battle, the Avengers regrouped on the helicarrier to meet with the Doctor, Clara, Fitz, and Nick Fury in order to discuss what to do next. However, the Hulk decided to abandon the team. Bruce Banner wanted to find solitary peace after the battle and flew away in a stolen quinjet. The team sat at a long table in a conference room where the TARDIS was parked to debate. The Doctor briefed them all about what was happening with the Zygons.

"Unfortunately," Fury said, "we can't have all the Avengers helping with the Zygons. Ultron just tried to wipe out mankind. We'll need some to help us deal with any aftermath of that, hunt down any spare robots that might've escaped, and deal with the press. The original Avengers have more experience, so I would think they should help with the Zygons and the newer people can stay behind."

By "newer people", Fury meant Falcon, Scarlet Witch, War Machine, and Vision. These new heroes all nodded their heads and agreed to do what Fury suggested.

"My wife is going to give birth to our third child soon and she's already stressed about the battle in Sokovia." Hawkeye said. "I need to be with her."

"We understand." Clara said. "You should be with her."

"And I will." Hawkeye said. "But I can't turn my back on my friends when they still need me. I'll help with the Zygons, but consider this my last mission."

"Me too." Iron Man said. "After this is over, I plan to leave the Avengers. I created Ultron and it almost destroyed the world, but so will these Zygons if I don't help you stop them."

"You can count on my help." Captain America said.

"And mine." Black Widow added.

"I will also assist before returning to Asgard." Thor said.

"The Zygons are on a plane to Moscow right now." The Doctor said. "Jack Harkness and Agent Simmons are already on board. They should be landing in a few hours. Good thing I have a time machine. Have a little rest and then we'll head off to Russia in the TARDIS. I know you've just done a lot with Ultron."

Clara then stepped out of the room to call Danny Pink on her cellphone. After a few rings he answered.

"What's up?" Danny asked. "Have you seen Sokovia on the news? It's devastating."

"Yes I'm very well aware actually. Are you anywhere near the Moscow airport?" Clara asked.

"Ya...How'd you know?" Danny asked.

"I didn't. I just need you to meet me there. I'll be there soon...in the TARDIS." Clara said,

"The TARDS!" Danny said. "Clara, you said you stopped traveling with him."

"I know. I'm so sorry." Clara said. "I promise I'll explain it all later and I won't lie about it. There's aliens coming to Moscow and they want to conquer the Earth. Please just meet me there and I'll tell you everything."

"Alright." Danny said. "I'll be there."

After the Avengers had some time to recuperate, they piled into the TARDIS with the Doctor, Fitz, and Clara. Fitz had been on the phone with Coulson, who said he may be able to send help, but it's unlikely, given that the situation with Jiaying has escalated and that they were now at war with the Inhumans. Nick Fury and the new Avengers watched the TARDIS fade away from the conference room on its way towards Russia, to fight the Zygons.

* * *

3W Institute 2015

From her office, Missy also watched the TARDIS disappear. Her army had grown quite sizably after the battle in Sokovia. She smiled, for soon, they would rise to attack the entire planet and no one would stand in her way. After all, even a Zygon is powerless to stop a Cyberman.


	15. The Original Avengers

Chapter 15: The Original Avengers

Moscow, Russia 2015

After a few hours in the air, the plane from London landed in Moscow. Jack Harkness and Agent Simmons snuck out of the Cargo hold and eventually found their way into the airport terminal. Unfortunately, by the time they go there, all the passengers had already left the plane. Jim and Tim, the two evil Zygons, we're now in Moscow with stolen time energy. They could've already changed their shapes already for all Jack or Jemma knew.

"What do we do now?" Simmons asked.

"Keep looking." Jack said.

Jack and Simmons walked around the terminal again with no sign of the two air stewardesses from London. Perhaps they had transformed back into the men in the passports they stole. When you're looking for shape shifters, it's like trying to find a needle in a hay stack, except it might not be a needle and you don't know what you're looking for. Jack and Jemma snuck outside on the grass next to the runways and still found nothing. They then laid down on the grass. There was a metal fence with many small holes near them that kept them inside the boundaries of the airport and allowed them to see what was beyond it.

"We can't just give up." Simmons said. "We sat with the cargo for three hours on a plane just to get here."

"They're probably already in the city for all we know." Jack said.

Suddenly, there was a slight breeze near where they were sitting followed by a loud wheezing noise. Jack and Simmons had both heard that sound before. Soon, the big, blue TARDIS materialized in the grass next to them. Jack and Simmons both promptly stood up. Soon, the Doctor, Clara, and Fitz came out of the TARDIS. Jemma ran to hug Fitz, who awkwardly hugged her back.

"Are you all alright?" Jemma asked.

"What happened?" Jack asked.

"Ultron isn't a problem anymore." The Doctor said.

"Did you get any of the Avengers to help?" Jack asked.

"Of course." The Doctor said. "I got the original Avengers."

Then, right on cue, Iron Man, Thor, Captain America, Black Widow, and Hawkeye exited the TARDIS.

"I wasn't sure when I'd come back to Russia." Black Widow said. "Nice to see you both again."

"Likewise." Simmons said.

"Where's the Hulk?" Jack asked.

"He's taking some time off." Captain America said.

"Clara!" A voice called from the other side of the fence.

Everyone turned towards the sound of the voice and saw Danny Pink standing there behind the fence. Clara rushed over to talk to him.

"Is that P.E.?" Fitz asked the Doctor. "Clara's boyfriend?"

"Yes." The Doctor replied.

The group then started to walk towards the fence.

"How did you know to come out here by the runways?" Clara asked when she finally reached Danny.

"I figured that TARDIS would arrive not in the middle of a busy airport where everyone could see it." Danny said. "You need to explain Clara. What's going on? James' party is tonight. I came here to celebrate with him, not to get dragged into another alien incursion."

"I only called because I wanted to be sure you were safe." Clara said.

Now, the Doctor, Jack, S.H.I.E.L.D. agents, and the Avengers all reached the fence.

"Oh my god." Danny said. "You were telling the truth. You really do know the Avengers."

"Hello." Iron Man said, still wearing his suit. "Want me to bring you over here?"

"Um...sure." Danny said.

Iron Man then flew over the fence, picked up Danny, and flew him back to the other side with everyone else.

"Thanks." Danny said. "I've been watching you on the news in Sokovia. What are you all doing here?"

"Helping to stop the Zygons." Hawkeye said.

"Zygons?" Danny asked. "I remember Clara telling me about them in London."

"These are different Zygons." Clara said. "The ones in London are the good ones. The two we're chasing, Jim and Tim, are the bad ones."

"Jim and Tim?" Danny asked skeptically.

"Apparently they took human names when they came to Earth." Jack said. "They stole time energy and they said they're going to use it to see they're family again."

The Doctor suddenly had a realization. This was not the first time he'd encountered Zygons in Russia. In fact, they were the same Zygons as last time.

"I know what they want." The Doctor said. "I can't believe I'm so stupid that I didn't remember it sooner."

"What is it?" Thor asked.

"It was two regenerations ago." The Doctor said. "How could I forget something like that!"

"Doctor!" Clara yelled. "Just tell us."

"Back in 1946, there were reports of a painting going up in an art museum in Moscow." The Doctor said. "Then people started disappearing. I decided to check it out. I wasn't the only one. I got there and found Agent Peggy Carter and some others investigating. Then three Zygons appeared. Two of them were Tim and Jim."

"Who was the other one?" Fitz asked.

"I don't remember." The Doctor said. "It was a female Zygon."

"Did you say Peggy Carter?" Captain America asked.

"Don't interrupt me again." The Doctor said to the Captain and the rest of the group. "The Zygons had a special interest in one of the paintings. I never found out why. I'm willing to guess that there are more Zygons trapped in that painting, just like with Elizabeth."

"So what else happened in 1946?" Clara asked

"The Zygons chased us outside." The Doctor said. "I don't remember all the details, but I do remember that I accidentally teleported the female Zygon to the center of the sun. I thought I killed Jim and Tim as well, but I guess not. They must have been hiding here all this time in Russia. They only came to London to get time energy. Now they're going to release their family."

"Do you remember what museum the painting is at?" Black Widow asked.

"Yes." The Doctor said. "I'll take us there in the TARDIS."

Just then, Fitz's cell phone began to ring. It was Agent Coulson.

"I have to take this." Fitz said.

Fitz then answered the phone. After a few minutes he hung up.

"What does Coulson want?" Simmons asked.

"Coulson?" Iron Man asked. "Isn't he dead."

Jemma felt like an idiot. She forgot that the Avengers thought Coulson was dead.

"Well the cat's out of the bag now." Fitz said.

"I don't understand." Hawkeye said.

"Fury needed you to believe that Coulson was dead so that you'd actually band together to stop Loki." Fitz said.

"We saw him die." Thor said.

"Fury wasn't ready to let him go." Simmons said. "S.H.I.E.L.D.'s project T.A.H.I.T.I. brought him back to life, with some side effects."

"He's running S.H.I.E.L.D. underground now." Fitz said.

"I don't believe it." Captain America said.

"It's the truth." Fitz said. "He just gave me some very bad news."

"What is it now?" The Doctor asked.

"Skye's mother is Jiaying." Fitz said. "She's been running a facility all these years that trains special people called Inhumans. We went to war with them earlier today. They've attacked the Illiad."

"What is the Illiad?" Thor asked.

"It's an aircraft carrier." Simmons said. "It's S.H.I.E.L.D. headquarters at the moment."

"That's not all." Fitz said. "Bobbi Morse was kidnapped."

"Who's that?" Black Widow asked.

"One of our best agents." Fitz said. "Coulson thinks Ward might've had something to do with it."

"Ward?" Captain America asked. "Isn't he on our side."

"He was working for H.Y.D.R.A. the whole time." Simmons said.

"I told Coulson we'd send help." Fitz said.

"Why couldn't you just tell him we're busy here with the Zygons?" The Doctor said. "Now, I'm going to have to leave because none of you can pilot the TARDIS!"

"We'll just split up." Jack said.

"Here's what's going to happen." The Doctor said. "We don't have time to waste so just do what I say. I'm taking Jack, Captain America, Thor, and Hawkeye to S.H.I.E.L.D. so we can assist them. I'll drop the rest of you off at the museum and you better take care of those Zygons."

"I said I didn't want to be dragged into this." Danny said.

"I don't care P.E." The Doctor said. "We're leaving. Get in the TARDIS or don't. It's your choice."

Danny did not want to abandon Clara if she was going into the city to fight Zygons. So, he boarded the TARDIS with everyone else. Then, the Doctor's time machine disappeared from the fields near the runways at the Moscow Airport.

* * *

3W Institute 2015

Missy watched from the screen in her office as the Doctor was once again forced to divide his team.

"I know your angry Doctor, but don't worry." Missy said. "I've got the perfect gift for you."


	16. Raina

Chapter 16: Raina

Moscow, Russia 2015

The TARDIS materialized in an alleyway downtown near the art museum where the Zygons were planning to unleash their entire criminal family and conquer the Earth. The doors opened and out stepped Clara Oswald, Danny Pink, Fitz, Simmons, Black Widow, and Iron Man. It was their mission to stop these evil Zygons, which would be hard to do, given that they could change their appearance at will. The TARDIS then dematerialized from Russia on its way to help S.H.I.E.L.D. with a war against the Inhumans under Jiaying and a kidnapping by former Agent Ward. The TARDIS was carrying the Doctor, Jack Harkness, Thor, Hawkeye, and Captain America. The Doctor was reluctant to go to S.H.I.E.L.D. instead of being there to stop the Zygons, but he had faith in his team in Russia and Jiaying could do incredible damage to the Earth if she conquered S.H.I.E.L.D. today. Back in Moscow outside the art museum, Simmons caught sight of two men in bright green coats. One was carrying a small suitcase. She recognized these men from the airport in London. This is how they looked before they changed their shape to become air stewardesses so that they could board the plane. The orb containing the stolen time energy was in the suitcase. The two men then entered the museum.

"That's them." Jemma said to the rest of the group. "The men in the green coats. Those are the Zygons. I recognize them from London."

"Then let's go get them." Black Widow said.

* * *

The Iliad 2015

The TARDIS reappeared inside Coulson's office as it had done before. This time, Coulson was waiting for it and he was not alone. Joining him was Agent Melinda May, Agent Lance Hunter, Agent Alphonso Mackenzie aka Mack, and Cal, Skye's father. The Doctor was the first one to step out.

"Doctor." Coulson said to the Time Lord. "Thank you for your help in Sokovia."

"You were right." May said. "He did get older."

"Nice to see you again too May." The Doctor said.

Soon, Jack, Thor, Hawkeye, and Captain America stepped out. The three Avengers were shocked to see that Coulson really was alive after all.

"What are they doing here!" Coulson yelled.

"We know you're alive." Hawkeye said. "Fitz told us everything."

"Well then hello." Coulson said to his Avengers friends. "This isn't how you were supposed to find out, but we'll deal with the consequences of that later I suppose. We could really use your help here."

"Hello May." Jack said.

Jack was remembering when he and May fought together in Manhattan during the Second Battle of New York against the Chitauri and the Daleks. They made a good team.

"Thank you all for coming." May said. "This is Hunter and Mack. I don't believe you've met them yet."

"I think I would've remembered meeting the Avengers." Mack said.

"I'm Cal." Cal said. "I'm Skye's father."

"Aren't Skye's parents evil or something?" The Doctor asked.

"You can make that argument." Cal said. "Her mother is planning on whipping out every human who doesn't have powers. Every bad thing I've done has been so I could get my family together. All she's done is rip it apart. Where are the other Avengers?"

"The others are still in Moscow stopping the Zygons." Captain America said. "We came here to help you."

"We've got two situations on hour hands." Coulson said. "The Inhumans have invaded this ship already and they've captured Skye. We need to rescue her and stop them."

"What are they even trying to do?" The Doctor asked.

"They want to know who else in the world is Inhuman." May said. "They're going to do that by spreading a blue chemical across the planet. Everyone who survives, is Inhuman."

"They'll wipe out over half the planet." Coulson said.

"What's the other situation?" Hawkeye asked.

"Agent Bobbi Morse was captured by Ward and Agent 33." Hunter said. "She's being held in a warehouse. They're likely to interrogate her thoroughly. We can't risk having our secrets spilled."

"He's also in love with her." May said.

"Why'd you have to say that in front of the Avengers?" Hunter asked.

"So we must split up once again?" Thor asked.

"I guess so." The Doctor said. "I'm staying here. The Inhuman threat is much more urgent."

"Then how are we supposed to get to the warehouse?" May asked.

"I'm very good at teleports." The Doctor said as he whipped out his sonic screwdriver. "I just need to know who's going."

"I am." May said. "I want to kill Ward myself."

"I'm going too." Hunter said. "There's no way I'm staying here instead of rescuing Bobbi."

"I'll go too." Captain America said.

"And me." Hawkeye said.

"That's enough." Coulson said. "Everyone else will stay here."

The Doctor then fidgeted with his sonic screwdriver for a moment until it was ready. May, Hunter, Captain America, and Hawkeye stood close together. Then, the Doctor pointed the sonic device at them and pressed the button. The four of them were then consumed by a bright light and disappeared. The Doctor had teleported them away.

"How did you know where to send them?" Mack asked.

"I didn't." The Doctor said. "May and Hunter know where it is. The sonic tapped into their minds, found the location, and brought them there."

"You didn't tell me the Doctor could do that." Mack said to Coulson.

"There's a lot of things I don't tell you." Coulson said. Coulson then looked around at the team of himself, Cal, the Doctor, Jack, Thor, and Mack. "Alright everyone. Let's go break Skye out of prison and save the world."

* * *

3W Institute 2015

Raina awoke suddenly. It was as though she had a nightmare. Unfortunately, it had all been real. She looked at her skin, which was still light green and spiked. She found herself sitting in a chair in a bright white office. In front of her was a desk and an empty chair at the other side of the desk. The last thing she remembered was being killed by Jiaying in Afterlife. That felt so real. How was she suddenly here? Where was here? She had no idea. Suddenly, the door to the room opened and in walked a tall woman in a purple coat and dress.

"Hello Raina." The woman said. "My name is Missy."

Missy then sat down in the empty chair behind the desk.

"Where am I?" Raina asked.

"You're in my office." Missy replied.

"How did I get here?" Raina asked.

"That is the tricky part." Missy said. "You died."

"I remember." Raina said. "Jiaying stabbed me, but I'm clearly not dead."

"Yes you are dear." Missy said. "Everyone's in denial at first, but you did die."

"Then how can I be here?" Raina said.

"Some special science." Missy said. "I could've just sent you straight to be upgraded, but I wanted to have this chat with you. You should be more appreciative."

"I don't understand." Raina said.

"Try to keep up dear. I don't have all day." Missy said. "The reason you're not a Cyberman is because I need you."

"Cyberman?" Raina asked. "Like those things that invaded the planet all those years ago? I remember it. I remember S.H.I.E.L.D. talking about that too. Something about Torchwood..."

"Never mind that." Missy said. "Those are the Cybermen I'm talking about. The dead have to go somewhere after all. The point is that you have a gift. I need that gift. I want to know the future."

"How do you know about me and my visions?" Raina asked.

"You ask too many questions." Missy said. "Just accept what's going on around you. We're going to be best girl friends, you and me. I'll tell you everything if you use your ability to see the future to help me."

"Ok." Raina said.

"Excellent." Missy replied with a grin.


	17. Victory of the Zygons part 1

Chapter 17: Victory of the Zygons part 1

Moscow, Russia 2015

After over four hundred years of waiting on Earth, the criminal Zygons, Jim and Tim, had gathered the time energy they needed in England to release their families from a painting in Russia. Once released, they would start to conquer the Earth and make it their new home, since the Time War destroyed their last one. These Zygons were different from the ones in English paintings that met Queen Elizabeth I. Those were the good Zygons: the politicians, the doctors, the policemen. The Zygons based in Russia were pure evil. The two Zygons were dressed in bright green clothes and had just walked into the crowded art museum in broad daylight where their painting was in storage in the basement. The painting had been in storage there since 1946. They planned to go to the basement, release their family, and start their invasion of Earth today. There was one small team of time travelers, S.H.I.E.L.D. agents, and Avengers here in Moscow that could stop them. They were Clara Oswald, Danny Pink, Jemma Simmons, Leo Fitz, Black Widow, and Iron Man. They saw the two Zygons enter the museum disguised as humans and they went in to stop them.

Following the Zygons through the museum was not easy when you were with Iron Man and Black Widow, who had just been all over the news for their part in stopping Ultron in Sokovia. Every time they tried to move, someone would come up to them and start speaking in Russian. Only Black Widow knew what they were saying. She told the group it was all praise and thanks. Natasha told all the people to back off. They were on a mission. Then, the two Zygons came to a door in a hallway that led to the basement. The team was on the other side of the hallway and could see the Zygons about to disappear. So, Iron Man flew into the air. He caught everybody's attention, including the Zygons. He then fired a laser blast at a window, causing the glass to shatter and explode.

"Everybody get out!" Tony shouted.

Although they could not fully understand him, the Russians in the hallway got the message and started running out of the hall, until only the Zygons and the team were left. Iron Man continued to hover in the air. The two Zygons were still disguised as humans. One of them was carrying a small briefcase that held the orb which contained the stolen time energy. Sensing a fight, they put the briefcase on the floor and transformed their bodies into their large, red, alien Zygon selves.

"How did you follow us here?" Jim asked.

"You were hard to miss in those green coats." Simmons said.

"For shape shifters," Clara said, "you don't do a good job of staying hidden."

Iron Man then extended his arms towards the Zygons and prepared to fire more laser blasts. Black Widow pulled out a small gun of her own and aimed it at the aliens. Simmons took out a gun as well and aimed it at the Zygons. She took this gun from the TARDIS when she and Jack were hunting the Zygons together back at the London airport. The gun Jemma had was special because it was a laser gun.

"I suppose you think you've won." Tim said.

"You're outnumbered and out-gunned." Fitz said. "I think we have won. Surrender."

"Never." Tim said.

Jim then opened the door to the basement, grabbed the briefcase with the time energy, and ran downstairs. Then, Tim's body started to morph and change again. This time, he started growing taller and taller until eventually, the Zygon had transformed itself into a Tyrannosaurus Rex. The dinosaur then let out a loud roar. It was going to fight and hopefully kill them while his brother released the Zygons below.

"It's a dinosaur!" Danny yelled.

"It's not the first one I've seen." Clara said, remembering the time there was a T-Rex trapped in Victorian London.

The T-Rex then started to walk forward.

"Run!" Black Widow yelled.

The five of them on the ground started to run away as the dinosaur approached. However, Iron Man started to fire his deadly lasers at it. They managed to slow the beast down and draw blood, but it kept moving. Tony stayed where he was and kept firing his laser blasts. Black Widow and Simmons then turned around and shot at the large T-Rex. Natasha shot bullets while Jemma shot lasers. Both were able to hit the T-Rex's legs, crippling it. Then, the T-Rex had sustained too much damage. It's body morphed back into a Zygon. The Zygon then fell to the floor. The team went over to check on it. They discovered that it was dead. Their attention was then drawn to the open door that led to the basement. Jim, the last remaining Zygon, had been given a head start.

"We're not done yet." Black Widow said. "Let's go."

* * *

Jim the Zygon ran through a hallway in the art museum's basement that was filled with sculptures, statues, and paintings all in storage. It looked similar to the halls in a WWII bunker in London. He looked through them all until he found the painting of a forest. Using Time Lord technology, Jim's Zygon children were placed in here to keep them safe. However, they were not frozen in time. Over four hundred years, they repopulated into countless generations. There were perhaps hundreds of thousands of Zygons in the painting now. So, Jim took out the glowing yellow orb that contained time energy. He was about to use it to release his children. He was also wearing a wrist communicator and pressed a button on it. He had a quick call to make.

"Are you there?" Jim asked into it.

"Yes." Jiaying said in response. "This better be important. I'm trying to fight S.H.I.E.L.D. so I can make more Inhumans for our plan."

"We have no more need for plan B." Jim said. "I'm here in Moscow with the time energy. I'm about to set the children free."

"Your wife would be proud." Jiaying said. "I'm happy, but I've worked too hard. My plan will wipe out humanity anyway. That will save us time. I'm not going to abandon the Inhuman project. I look forward to seeing generations of Zygons emerge onto this world."

"So do I." Jim said.

Jiaying then hung up. After she did, Jim the Zygon started the process of using the time energy to release the hundreds of thousands of evil Zygons trapped inside the painting.


	18. Inhumans

Chapter 18: Inhumans

The Iliad 2015

The Doctor, Agent Coulson, Jack Harkness, Mack, Thor, and Cal walked through the halls of the Iliad. Jiaying and her Inhumans had conquered a certain portion of the ship. It was also where they were keeping Skye prisoner. Their first objective was to free her. Then they would work together to stop Jiaying. They soon came to a long hallway. At the end of the hallway, they could see Skye sitting behind bars. Unfortunately there was an Inhuman standing in front of the prison cell. She was a tall woman with red hair.

"It's just one Inhuman." Coulson said. "This shouldn't be too hard."

"You say that now." Mack said. "Wait until you see what she can do."

Suddenly, there were two red haired women standing in the way. It happened so fast, that the others were barely able to see it. Apparently, this Inhuman had the ability to multiply herself. Then, there were three, four, and five copies of the red haired woman. The five identical women then charged at the S.H.I.E.L.D. team to engage in hand to hand combat. Coulson, Jack, Mack, Thor, and Cal charged forward and were soon each locked in combat with one of the copies. The Doctor, never a good fighter, turned around walked away from the fight. He went just around the corner and took out his sonic screwdriver, trying to figure out what he could do to help. Perhaps, he could unlock Skye's prison from here and then she could help. While he was thinking, a handsome young man walked up to him.

"Are you with S.H.I.E.L.D.?" The man asked.

"Who are you?" The Doctor asked.

"I'm Lincoln." He said. "I came here to fight S.H.I.E.L.D. with the other Inhumans, but then I discovered Jiaying's plan to destroy all normal humans and I rushed down here to free Skye so we could stop her."

"Oh good. I'm sure we could use your help." The Doctor said.

Lincoln then looked over the corner at the fight that was going on down the hall.

"Your friends are fighting Alisha." Lincoln said. "They need to take out the original and other copies will follow."

Lincoln then ran down the hallway to assist in the fight and tell everyone Alisha's weakness. The Doctor then looked back down at his sonic screwdriver. When he looked back up, there was a woman standing in front of him. She was Chinese in origin and she had a scar on her face.

"Hello Doctor." She said.

The Doctor then pointed the screwdriver at the woman and scanned her up and down. He then looked at the device and found some strange readings.

"Have we met before?" The Time Lord asked.

"No." She said. "You have met some of my associates though."

"Who would they be?" The Doctor asked.

"Jim and Tim." Jiaying said. "I just got a call from Moscow. They're about to succeed with their plan."

"Who are you?" The Doctor asked. "Are you this Jiaying woman I keep hearing about?"

"Yes." She replied.

"What are you doing working with the Zygons in Russia?" The Doctor asked.

"I've been working with the Zygons for over fifty years." Jiaying said. "I'm older than I look."

"So am I." The Doctor said. He looked at the readings on the sonic screwdriver again. "You're not human."

"That's where the term Inhuman comes from." Jiaying said. "None of us are traditional humans."

"No. There's something else." The Doctor said. "You're not from this planet."

"Well it looks like you've discovered my secret." Jiaying said. "I don't see a point in hiding now."

Suddenly, Jiaying's body started to morph and change. Her skin turned red and she started to grow and expand. Within seconds, Jiaying had transformed into a Zygon.

"That doesn't make sense." The Doctor said. "What do the Zygons want with Inhumans?"

"They were our plan B." Jiaying said. "In case our original plan doesn't work."

"You just said your plan was about to work." The Doctor said. "Why would you still wipe out the human race?"

"I worked too hard to just quit now." She said.

"Jiaying was a real person. She gave birth to Skye. Where is she now?" The Doctor asked.

"I killed her a long time ago." The Zygon said. "I've been impersonating her all this time. I can't let you ruin everything for me. I'm sorry to say that I've come here to kill you."

Jiaying and the Doctor then heard victorious shouting coming from the hallway behind them. Jiaying peeped her Zygon head over the corner and saw that all Alisha's clones were unconscious and that Lincoln was bringing Skye out of her prison containment. She was also shocked to see Thor, a powerful Avenger. Instead of killing the Doctor, she decided to run away and enact her evil plan before anyone could stop her. The Doctor then turned and ran down into the hallway. Skye was wearing special gloves that rendered her powerless. Lincoln ripped them off, giving Skye back her Inhuman powers. She was overjoyed to see Coulson, Mack, her father again. She was also happy to see Jack Harkness and Thor. She had traveled with them in the TARDIS for a brief time before working with them to stop the Dalek-Chitauri Invasion. She was happy they had come to her aid. She figured the Doctor couldn't be too far away. Then, she saw an old man running down the hall.

"Who's this?" Skye asked.

"Skye, it's me." He said. "The Doctor."

"The Doctor isn't an old man." Skye said.

"I regenerated." The Doctor said. "I'll explain what that means to all of you later. Just know that it's me."

"It's true." Coulson said to Skye. "He even helped the Avengers defeat Ultron."

"I have some bad news." The Doctor said. "In addition to this, we're also dealing with a Zygon problem Skye."

"Zygon?" Skye asked.

"Shape shifting aliens." The Doctor said. "We have another team in Moscow right now that's fighting them."

"What about here?" Skye asked. "We have to stop my mother. That's our top priority."

"That's just the thing." The Doctor said. "Jiaying has been working with the Zygons. The Inhumans were their plan B in case their initial plan didn't work out."

"I don't understand." Skye said.

"That's not even the worst part." The Doctor said. "This may be hard to hear, but it's the truth. Jiaying is a Zygon."

"You can't be serious." Lincoln said.

"I just saw her. She came down here to kill me. Then she saw that you all beat that Inhuman girl and freed Skye. I think she ran off to initiate her plan before we could stop her. She told me that she killed the real Jiaying years ago and that the Zygon has just been masquerading as her this whole time."

"Ok." Skye said. "Jiaying is an alien. She's not my real mom. That will make it easier for me to kill her."

"We have to get outside." Coulson said. "That's where she'll be."

"There's one more thing." The Doctor said. "Jiaying said that the Zygons in Moscow were about to succeed."

While the group processed this information and rushed through the ship to get outside, Agent May, Agent Hunter, Captain America, and Hawkeye were arriving at a warehouse to fight Grant Ward and rescue Bobbi Morse. However, the Master was about to arrive and make a special deal with former Agent Ward.


	19. The Master's New Companion

Chapter 19: The Master's New Companion

United States 2015

They didn't know how he did it, but the Doctor certainly did it. He was able to transport Agent May, Agent Hunter, Captain America, and Hawkeye to a warehouse on the mainland where Ward and Agent 33 had kidnapped Agent Bobbi Morse. The goal was to rescue her and take out Ward in the process. Agent 33 or Kara, had been using special technology to change her face. She typically chose to go around disguised as Agent May. Today would be no different. This small team of S.H.I.E.L.D. agents and Avengers walked cautiously into the main entrance of the abandoned warehouse.

* * *

On the top floor of the warehouse was a large room. Agent Bobbi Morse was strapped to a chair and gagged so she couldn't speak. Grant Ward was about to rig a gun so that when someone opened the door to rescue Bobbi, they would be shot. Agent 33 stood in the room, disguised as Melinda May and watched. Ward was about to finish rigging the weapon, when suddenly there was a bright flash of light in the room. When the light went away, a tall woman in a purple coat and dress was standing there. Her name was Missy and she had just teleported into the room. Ward and Kara instinctively took out their guns and aimed them at the strange new woman.

"Hello dears." She said. "My name is Missy. I've been watching you two for some time and I believe that now we can help each other. You don't want S.H.I.E.L.D. to get little Bobbi and my boys need fighting practice. Let's team up. It's a win-win."

"You'll have to be more specific than Missy." Ward said. "Why shouldn't we just kill you right now?"

"You can't for starters." Missy said. "If you shoot me, I'll just pop right back, probably with a new face."

"You're a Time Lord." Ward said.

"Time Lady." Missy said. "I'm old fashioned."

"H.Y.D.R.A. has some files on the Doctor and his regenerations." Ward said. "Are you the Doctor?"

"Haven't you been paying any attention?" She asked. "My name is Missy. The Doctor is my old friend. I'm not here to stop you, I'm here to help you. Two S.H.I.E.L.D. agents and two Avengers just walked in through the front door. Two of you and some guns aren't going to do the trick. I want to help you and let my boys get some exercise."

"Who are your boys?" Kara asked.

"Cybermen." Missy replied.

* * *

May, Hunter, Hawkeye, and Captain America proceeded with caution as the walked up the stairs to the first floor of the warehouse. May and Hunter both held their guns, ready to fire at a moment's notice. Hawkeye had a bow and arrow at the ready and the a Captain held his shield. They came to a long hallway on the first level. Suddenly, there were two flashes of light at the end of the hall. When the lights disappeared, two Cybermen were standing there. They prepared their wrist lasers to fire deadly blasts at the four humans. May remembered the last time she saw a Cyberman. It wasn't when they invaded the Earth in 2007. It was when she was in New York City in 2013. Her S.H.I.E.L.D. team was hunting a Weeping Angel in abandoned subway tunnels under the city. Their search for the Angel led them to a Cyberman instead. They quickly met the eleventh Doctor and Clara Oswald for the first time, who were in New York for the same purpose. They managed to destroy that Cyberman, but now two of them appeared out of nowhere two years later.

"What is that?" Captain America asked. He had not been awake when the army of ghosts across the planet turned out to be Cybermen and invaded.

"Cybermen." Hunter said. "Bullets don't affect them."

The two Cybermen then fired lasers at them. However, Captain America stepped in front. The blasts hit his special shield. He then threw the shield like a frisbee towards the Cybermen, it completely ripped though one of them and shredded it to pieces. Hawkeye took out an explosive arrow and fired it at the other Cyberman. It hit directly, causing a small explosion that destroyed the Cyberman. The four of them than ran to the end of the hall. The Captain picked up his shield on the way. They found another staircase and climbed it until they reached the top floor and came to an identical hallway.

On the other side of a door at the end of the hallway, Ward, Kara, and Missy stood while Bobbi Morse sat in a chair. All the team had to do was get to the door and rescue her. However, there were two Cybermen guarding the entrance. The team moved forward until they were in the center of the hall. However, the Cybermen did not attack them. Then, two more Cybermen teleported at the other end of the hall by the stairs. The S.H.I.E.L.D. team was now trapped between Cybermen on both sides of the hall. They extended their lasers as if to fire more powerful blasts. The Captain's shield could not protect them all this time. Then, the Cybermen fired, but they did not fire lasers. Instead, a pink gas shot out of their guns and raced towards the humans. As they breathed in the pink gas, they suddenly fell to the ground unconscious. In the other room, Missy, Ward, Kara, and Bobbi heard their bodies drop to the floor in the hall.

"Looks like my boys did their job." Missy said. "Now comes the fun part."

Missy then pulled out a laser gun from her coat pocket and aimed it at Kara.

"What are you doing!" Ward shouted.

"Say something nice." Missy said.

"What?" Kara asked.

"Say. Something. Nice." Missy said.

"You...are very pretty." Kara said.

"Thank you dear." Missy said.

Missy then fired a laser blast at Kara and disintegrated her body.

"What did you just do!" Ward yelled.

"She was annoying." Missy said. "Besides, I have bigger plans for you, if you're up for it."

"I don't want anything to do with you!" Ward shouted.

"What if I told you that you could see the universe?" Missy said.

"What?" Ward asked.

"The Doctor always has his companions running around to help him out. I want one too. You, my friend, are both cute and dangerous, the perfect combination. What do you say? You want to see the stars? I'll have to leave this planet very soon. I'd like you to come with me." Missy said.

"Where would we go?" Ward asked.

"Anywhere and everywhere." Missy said. "Our first stop will be Asgard. I have a friend there I've been dying to visit."

Ward thought about his situation. There wasn't really an organized H.Y.D.R.A. anymore that he was aware of. Kara had just died. He couldn't exactly go back to S.H.I.E.L.D. anymore.

"Ok." Ward said. "I'll go with you."

"Excellent." Missy said.

Missy then pressed a button on her vortex manipulator that she wore on her wrist. Then, she, Ward, Bobbi, May, Hunter, Hawkeye, and Captain America were all transported from the warehouse to the 3W Institute. Here, Missy had a devious plan for the unconscious heroes. Meanwhile in Russia, it seemed that nothing could stop the Zygon army from rising.


	20. Victory of the Zygons part 2

Chapter 20: Victory of the Zygons part 2

Moscow, Russia 2015

In an art museum in the middle of downtown Moscow, people ran out into the streets. There had been an intense battle between the Zygons and a coalition of time travelers, S.H.I.E.L.D. agents, and Avengers inside the museum. The police soon gathered around outside the museum, but did not dare enter yet until they understood exactly what was happening. Inside the museum, Tim the Zygon was dead, defeated by Agent Simmons, Black Widow, and Iron Man. The others who were there were Clara Oswald, Danny Pink, and Agent Fitz. The Zygons had a painting stored in the basement for many years. Inside were hundreds of thousands Zygons, perhaps there were even millions. They were sent there using stolen Time Lord technology to hide in the paintings until the twenty first century when they would come out and conquer the Earth. Jim the Zygon had run downstairs into the basement during the battle to begin the process of releasing his Zygon family. Once they killed the other Zygon, the team rushed downstairs to stop him. The basement was dark and filled with sculptures and paintings sitting in storage.

"He could be anywhere." Danny said.

"We have to keep looking." Iron Man said. "He's definitely here somewhere."

The team cautiously roamed the halls of the museum basement looking for the Zygon. Iron Man had his blisters ready. Black Widow had her two hand guns ready as well. Agent Simmons was carrying a laser gun that she took from the TARDIS. Clara, Danny, and Fitz were unarmed, but still wanted to help in any way they could. The basement was immense. It felt like they would never find anything. Finally, they came to a particular long hallway. At the end of the hallway they saw something strange. There was a painting on the floor and it was glowing bright yellow. Next to the painting was the bright yellow orb that contained the stolen time energy. Jim the Zygon was standing in front of it. The team ran down the hall to fight him, but then stopped about halfway. They aimed their weapons at Jim.

"What have you done?" Clara asked.

"I've started the process. I've opened the time energy in the orb. It's reaching inside the painting to pull out my Zygon children as we speak. As much as I hate the Time Lords, I must say they made excellent technology." Jim said.

"Stop it now!" Fitz yelled.

"No." Jim said.

"Do it or well shoot you down." Simmons said. "You're brother is already dead upstairs."

"A necessary sacrifice." Jim said. "Go ahead and shoot me. It doesn't matter. The process is irreversible. The Zygons are coming and there's nothing you can do to stop us. We are victorious."

Iron Man then fired a laser blast at Jim. It hit the alien in the chest and he dropped dead to the ground.

"Why did you do that?" Clara yelled. "He was the only one who knew how to stop it."

"He said it couldn't be stopped." Iron Man said.

Unfortunately, Jim was right. Suddenly, there was a bright flash of light coming from the orb. When it faded, a single Zygon stood in its place. It had been trapped inside that painting for over four hundred years. It was ready to hunt. Then, there was a second flash of light that brought a second Zygon. Soon, more and more Zygons started appearing.

"Run!" Black Widow shouted.

The team turned around and ran out of the basement as fast as they could. They gave it their best effort, but they could not stop the Zygons from fulfilling their task. An army of millions would soon erupt out of that painting. The Zygons did not follow the humans at first. They decided to wait until at least a hundred had come out of the painting before starting their attack on humanity. The human team soon reached the front entrance to the museum. They looked outside and saw police and frightened citizens standing outside.

"What do we do now?" Fitz asked.

"Call the Doctor." Black Widow said.

Clara pulled out her cell phone and called the Doctor. After a few rings, he answered.

"Clara." The Doctor said. "Things aren't going as we planned here. There's something I have to tell you about Jiaying and the Zygons."

"My news is more important Doctor." Clara said. "Jim and Tim are dead, but we couldn't stop them from completing their plans. The Zygons are out. There will be millions of them pouring into Moscow any minute. Then they'll spread out across the world."


	21. The Army Rises

Chapter 21: The Army Rises

The Iliad 2015

The Doctor, Jack, Coulson, Skye, Mack, Cal, Lincoln, and Thor rushed through the halls of the aircraft carrier to get on deck. Jiaying, who was revealed to be a Zygon in disguise, was already there with Gordon, a blind inhuman with powers of teleportation. They had a briefcase filed with a blue chemical that will wipe out the human race and leave only inhumans if exposed. So, it was imperative that the team stop them. Eventually, they made it outside and found Jiaying and Gordon alone in the center of the deck. They were inspecting the contents of the briefcase. They swiftly shut it when they saw the entire team arrive and stand by the doorway.

"You're too late." Jiaying said.

Coulson and Mack held small guns and aimed them at the two of them. Skye and Lincoln aimed their hands and we're ready to unleash their powers. Thor had his hammer and the Doctor had his sonic screwdriver.

"Is it true?" Skye yelled to Jiaying. "Have you been lying to me? Are you really a Zygon?"

Jiaying had a look of disappointment on her face. Instead of answering Skye, she decided to show her. Jiaying's body started to morph and change until she became a tall, red Zygon.

"It's true." The Zygon Jiaying said to Skye. "You're mother died a long time ago. I've just been impersonating her."

"You're outnumbered." Coulson shouted. "Stop this now."

"Never." Jiaying said.

Suddenly, a bright blue light energy surrounded Gordon and he disappeared. He teleported somewhere. Gordon suddenly reappeared behind the team and began fighting them. He teleported at rapid speed to each member of the team and attacked them. Gordon single handedly created a frenzy of confusion around them so that their attention was no longer on Jiaying. The Doctor had enough of this. Gordon appeared in front of the Time Lord. The Doctor quickly pointed his screwdriver at Gordon and activated it. Then, Gordon tried to teleport away, but found that he couldn't. The sonic technology was interfering with his abilities. Then, Gordon started to glow bright blue. After a few seconds, he was consumed by a small explosion of blue energy and disappeared.

"Did he teleport?" Thor asked.

"No." The Doctor said. "He's dead."

The group then turned their attention back to the Zygon Jiaying, who was running towards one of the Quinjets. Coulson took a careful aim and then fired his gun at her. The bullet from Coulson's gun hit Jiaying in the arm. It caused her to let go of the briefcase, which slid across the deck and fell into the ocean.

"No!" Jiaying shouted.

Her plans were now ruined. She would survive being shot in the arm by a bullet. The Zygon Jiaying then pulled out a laser gun that she was concealing and aimed it at the S.H.I.E.L.D. team. Just one blast would kill whomever it hit, except perhaps Thor.

"Put it down!" The Doctor yelled to her. "It's over."

"You'll pay for this!" Jiaying yelled.

She then fired the laser gun. A yellow laser blast shot out of the gun and hit Cal. He then dropped dead to the ground.

"No!" Skye yelled.

Jiaying then pressed a button on her vortex manipulator and transported herself away from the ship. Skye knelt down to be with her dead father. They had saved the world, but Jiaying had escaped and no one knew where she would go. The blue chemicals fell into the water, and would silently leak their way into the fish and later into the human populace. However, that was a problem for another day. Now, the Doctor was getting a call from Clara in Moscow on his cell phone. So, he answered it.

"Clara." The Doctor said. "Things aren't going as we planned here. There's something I have to tell you about Jiaying and the Zygons."

"My news is more important Doctor." Clara said. "Jim and Tim are dead, but we couldn't stop them from completing their plans. The Zygons are out. There will be millions of them pouring into Moscow any minute. Then they'll spread out across the world."

"Try your best to contain them." The Doctor said. "I'll get Agent May, Captain America, and the others and then we'll be in Moscow soon. Good luck Clara. Be careful."

The Doctor then hung up.

"What's going on?" Thor asked.

"The Zygons are out." The Doctor said. "Millions of them are going to crowd into Moscow soon. If they aren't stopped, they'll spread to the rest of the world."

"Sounds like we're going to Moscow." Lincoln said.

"We have to get the rest of our team first." Coulson said.

* * *

3W Institute 2015

Neither Coulson nor the Doctor knew that Captain America, Hawkeye, Agent May, Hunter, and Bobbi had all been kidnapped by Missy and Ward and brought to the 3W Institute. Ward had agreed to be Missy's new companion, something they were both excited about. Now, Missy sat in her white office at her desk. Across from her, Raina and Ward sat.

"I called you both here for a special reason." Missy said. "Raina's had a vision."

"I saw Zygons." Raina said. "They're about to invade Moscow in the millions, but the Russians won't be able to contain them. They'll spread across the world."

"What does that mean for us?" Ward asked.

"It means we have to act quickly." Missy said. "Our plans mean nothing if the Zygons conquer Earth. So, we have to do it before they have the chance."

"So what are you going to do?" Raina asked.

"I'm going to raise my army of Cybermen." Missy said. "Today."

Missy had already started the process of waking her army. The Cybermen had been kept in chairs that were inside tanks. Now, the tanks had been emptied of water and Cybermen. There were six tanks however, still being used. However, none of them had any of 3W's dark water in them. The tanks now functioned as prisons. Unconscious and strapped to a chair in each tank was Captain America, Hawkeye, Agent May, Hunter, and Bobbi. The sixth tank had something else inside. It was a Cyberman. However, this Cyberman was not silver. It was black. Missy brought Ward and Raina down this hallway to check on the black Cyberman.

"What is that Cyberman for?" Ward asked.

"It's a little side project of mine." Missy said. "Earth is defended by the Doctor and those superheroes in the Avengers. I need a Cyberman that can handle them."

"What?" Raina asked.

"He's still developing now." Missy said. "When I'm done with him, I'll have my very own super Cyberman."


	22. The Battle of Moscow

Chapter 22: The Battle of Moscow

Moscow, Russia 2015

Clara, Danny, Fitz, Simmons, Black Widow, and Iron Man ran out of the art museum. Police had already arrived on the scene when they heard reports of shooting. Scared civilians crowded behind the police cars. Natasha, being the only one who spoke Russian, went ahead to explain the situation to the police, while the rest of the team stood by.

"What did the Doctor say?" Tony asked.

"He said to try and contain the Zygons to Moscow." Clara said. "He's going to pick up everyone else in the TARDIS and then they'll all come here to give us reinforcements."

The police looked skeptically at Black Widow when she finished her story, but they soon realized that she was telling the truth when dozens of Zygons started to run out of the museum. Iron Man flew into the sky. Fitz, Simmons, Clara, Danny, and Natasha ran behind the police. The police started shooting at the aliens as they exited the museum, killing many of them before they had a chance to make it past the front steps. Iron Man shot them from above with his laser blasts. Clara and the others started yelling to the hundreds of civilians in the streets to run away. While not all of them could understand English, they got the message. The civilians started to run away.

The police continued to shoot the Zygons, but eventually, they ran out of bullets. Then, huge numbers of Zygons were now able to run past the museum steps and attack the police. Tony couldn't shoot them all from above. Black Widow and rest of the team ran away to get a secure position. There, they could use their weapons to attack the Zygons. Natasha had multiple guns. She gave one to Danny, who had fought in a war zone before. Simmons held a laser gun that she took from the TARDIS. Chaos reigned now throughout the city as the Zygons pillaged everything they could. Within twenty minutes of the attack, the Russian military was called in to fight. Tanks raced through the streets of Moscow blasting and killing many Zygons. Helicopters filled the air, shooting down the aliens from above. However, more and more Zygons continued to pile out of the art museum and rip through downtown.

In the streets, Black Widow, Iron Man, Danny, and Simmons worked with the army to shoot the aliens. Clara and Fitz each found baseball bats and used those as weapons to attack any Zygons that approached them. The largest city in Russia (and the second largest city in Europe after Istanbul) had become a war zone. There were over twelve million people in this city and the Zygons were determined to destroy every one of them and then spread out to conquer the planet. Suddenly, Clara's cell phone started to ring. She saw that it was the Doctor and answered it.

"Where are you?" Clara yelled. "We need you here!"

"I've been trying to locate Captain America, Hawkeye, Agent May, and Hunter, but they aren't at the warehouse." The Doctor said.

"So where are they?" Clara asked.

"Where do people go when they die?" The Doctor asked.

"What?" Clara asked. "I don't know."

"Neither do I, but according to the TARDIS that's where they are." The Doctor said. "I'm literally going to hell Clara. I be back as soon as I can."

"Just be careful." Clara said.

She then hung up the phone and continued running through the streets of Moscow amidst an alien invasion with only a baseball bat to defend herself. Unfortunately, Clara and everyone else in Moscow and across the world did not know that the situation was about to get a whole lot worse. It was the middle of the day in Moscow, but suddenly, it became much darker. Dark clouds filled the sky. Then, a black rain fell from them, but only in certain places, over graveyards and morgues. Slowly, throughout graveyards in Moscow and across the world, the dead began rising from their graves. However, they did not return as zombie humans. Instead, they returned as an army of Cybermen.


	23. The Underworld

Chapter 23: The Underworld

The Iliad 2015

The Doctor, Skye, Jack, Coulson, and Thor gathered themselves together. They had just saved the world from Jiaying's death serum (for now anyway). Unfortunately, Jiaying teleported away and Cal was dead. The worst news was from Clara Oswald, who called from Moscow to say that an army of millions of Zygons had been unleashed onto the city and would spread across the world if it was not contained. The Doctor needed to get to Moscow, but he wanted to get the other members of his team that had went to rescue Bobbi Morse first. After all, two of them were Avengers. So, the Doctor, Skye, Jack, Coulson, and Thor boarded the TARDIS inside the ship's lower levels. Lincoln and Mack stayed behind to put things in place with S.H.I.E.L.D. on the ship. The TARDIS soon disappeared.

"I've set the TARDIS to locate Agent May and the others." The Doctor said. He looked at the screen and fell silent. Agent May, Hunter, Captain America, and Hawkeye were not at the warehouse. They were somewhere else. "That's impossible."

"What is it?" Coulson asked.

"Where are they?" Skye asked.

"I have to call Clara." The Doctor said as he pulled out his phone and called her. Clara picked up, but she was angry. She was in the middle of a battlefield in Moscow between humans and Zygons.

"Where are you?" Clara yelled. "We need you here!"

"I've been trying to locate Captain America, Hawkeye, Agent May, and Hunter, but they aren't at the warehouse." The Doctor said.

"So where are they?" Clara asked.

"Where do people go when they die?" The Doctor asked.

"What?" Clara asked. "I don't know."

"Neither do I, but according to the TARDIS that's where they are." The Doctor said. "I'm literally going to hell Clara. I be back as soon as I can."

"Just be careful." Clara said.

Clara then hung up.

"We're going to the underworld?" Thor asked.

"I finally get to know what happens after death." Jack said, making light of the fact that he's never stayed dead for long. His joke amused everyone for a moment. Then they remembered the severity of where they were going.

"Are they dead?" Coulson asked.

"I don't know." The Doctor said.

"How else could they have gone to such a place?" Thor asked.

"We're about to go there in the TARDIS and we're all still alive." The Doctor said. "Let's just be careful."

The TARDIS then locked on to the coordinates and transported there.

"We landed." Skye said. "I've been around this box enough times to know when we've landed."

The Doctor cautiously opened the doors and stepped out into a dark hallway. The others soon joined him.

"What is this place?" Jack asked.

"Let's find out." The Doctor said.

They continued walking down the hall and found what they were looking for. On one side of the hallway were empty tanks. Inside each tank (unconscious and strapped to a chair) was Agent May, Hunter, Captain America, Hawkeye, and Bobbi. A final tank at the end of the hallway had a black Cyberman inside, but the team hadn't gotten that far yet.

"They're alive." Skye said. "I can see them breathing."

Suddenly, Missy, Ward, and Raina walked into the hall through a door and stood next to the tank with the black Cyberman at the end of the hall.

"Hello Doctor." Missy said.

"You!" Skye yelled to Ward. "You did this!"

"As much as I would like to claim responsibility for this, the true genius was Missy's." Ward said.

"Thank you dear." Missy said.

"Who are you?" The Doctor asked.

"You don't remember?" Missy asked. "I'll give you a hint. I'm a Time Lady."

"Which Time Lady?" The Doctor asked.

"The one who saved your life back on Earth when Rassilon almost killed you and Gallifrey fell from the sky." Missy said.

"No." The Doctor said. "It can't be. Your name is Missy?"

"Oh try to keep up." She said. "It's short for Mistress. I couldn't very well keep calling myself the Master, now could I?"

"No." Jack said. He remembered the Master all to well back when...she was Harold Saxon. "The Master is dead. I watched him die."

"I could say the same of you." Missy said.

"Who is the Master?" Thor asked.

"An evil Time Lord." Coulson said. "S.H.I.E.L.D. has files on many of his past incursions on Earth."

"Where are we?" The Doctor asked.

"The 3W Institute." Missy said. "Founded by a man many years ago who could hear the dead. He set up a place for their minds to go. I've added some Time Lord technology to the mix. Download the minds into a data cloud and upgrade the bodies into Cybermen."

"Cybermen!" The Doctor and Coulson yelled at the same time.

It was only now that Skye realized that Raina was standing next to Missy and Ward.

"Raina?" Skye asked. "You're alive?"

"That's a weird technicality." Missy said. "Usually I just upgrade the dead, but Raina here is special. Her visions have become something very useful to me."

"I watched Jiaying stab you in the neck." Skye said. "How can you just be standing here."

"I'm not immortal." Raina said. "I've been given a second chance. However, if I die a second time, it's permanent."

"What's Ward doing here?" Coulson asked.

"I need a companion." Missy said. "The Doctor's always got one. Why can't I? How is dear Clara holding up in Moscow? She'll find it even more difficult to fight when my Cybermen finally get there."

"How do you know about her?" The Doctor asked.

"I brought you two together." Missy said. "The woman in the shop? The mysterious message from the paper in Victorian London? All of it was me."

"You're even more insane than before." The Doctor said.

"I made something." Missy said.

The glass in the waterless tank next to her opened and out stepped a black Cyberman.

"You've changed the color." The Doctor said.

"I've done more than that." Missy said. "This is a Super Cyberman, powerful enough to fight the Avengers. Or at least he will be once he gets into action. This Cyberman has the ability to absorb powers. I kept these five in tanks to see what it could take from them. As of now, it has Captain America's enhanced fighting skills, speed, and strength as well as Hawkeye's accuracy and agility. While I've been talking, it's been scanning and copying Thor and Skye's powers. I can't wait until it copies all the Avengers, especially Vision."

Thor stepped forward and threw his hammer at the Super Cyberman at lightning speed. It would surely destroy the metal creature. However, the black Cyberman extended its arm and caught the hammer in its hand. It had scanned and copied Thor's strength.

"That's impossible." Thor said.

The Super Cyberman then threw the hammer at lightning speed towards Skye, before she could use her powers to do anything. Thor stepped in front of her and caught the hammer just in time to save her.

"Now I need to talk to the Doctor alone." Missy said as she pulled out a laser gun and aimed it at the team.

"Your weapon can't kill me." Thor said.

"It's not designed to." Missy said. "My boys in the lab have been working very hard on this. They combined the powers of a laser gun and a vortex manipulator. One hit, and you'll be sent to a random spot back in time. It's like a Weeping Angel without all the mess. Now, say something nice."

Thor ran towards Missy to knock the device out of her hand. So, Missy fired the weapon. A blue energy beam shot out of the gun and hit Thor directly. He was consumed by a blue light and then disappeared back in time. Missy did the same thing to Jack, Skye, and Coulson. The Doctor now stood alone while four of his friends were trapped somewhere in the past.

"Where did you send them!" The Doctor yelled.

"I don't know." Missy said. "It's all random. They could be anywhere, but that doesn't matter. Black rain is falling on the Earth as we speak. My Cybermen are rising."


	24. Agent Carter and Agent Coulson

Chapter 24: Agent Carter and Agent Coulson

New York City, United States 1947

It happened instantly. One second, Thor, Jack Harkness, Skye, and Phil Coulson were standing with the Doctor in a hallway in the 3W Institute confronting Missy, Agent Ward, Raina, and the Super Cyberman. Then, Missy zapped them with a special gun she developed that sends people back in time. They suddenly found themselves in a dark alleyway. They heard the sounds of cars and people coming from the nearby street. It was dark. Wherever they were, it was night. The four of them then walked out onto the sidewalk and instantly recognized that they were in Manhattan. Judging by the clothes of the people and the cars on the street, they guessed that they were in the 1940's or 1950's. Jack had been to New York City a few times throughout the years doing missions for Torchwood and he was last here during the Second Battle of New York against the Chitauri and the Daleks in 2013. He figured it was more like the 1940's. The four of them seemed out of place in this time with their clothes. Thor looked especially out of place. However, people on the street passed them by. Only one woman stopped to look at them. Her name was Peggy Carter.

"Excuse me?" Peggy Carter said as she approached them. "Are you all right? I saw a flash of blue light in the alley."

"Oh ya." Skye said, still in shock that they had been sent back in time. "We're all fine."

"What year is it?" Jack asked.

"1947." Peggy said. "You must be from the future."

"You are familiar with time travel?" Thor asked.

"Not personally, but some time travelers recently helped me with an alien problem in Russia. That's right. I know about aliens too. I'm Agent Peggy Carter. You might as well just tell me who you are. It's obvious that your not from Earth, at least not the present Earth."

"You're Peggy Carter!" Coulson said. "My name is Agent Phil Coulson. I've been the Director of the S.H.I.E.L.D. since 2014."

"How does she know about S.H.I.E.L.D.?" Thor asked.

"I'm one of its founders." Peggy said. "It's nice to know S.H.I.E.L.D. is still around in the future. Tell me. Were you ever able to defeat H.Y.D.R.A.?"

"That's a complicated story." Jack said.

"Never mind." Peggy said. "I don't want to know. What are you all doing here?"

"It wasn't intentional." Jack said. "We were sent here by a crazy woman so we wouldn't be around in the future to stop her conquest of Earth."

"That's just the Cybermen." Skye said. "Clara said that the Zygons had already invaded Moscow."

"Zygons in Moscow." Peggy repeated. "There's a sentence I never thought anyone would ever say again."

"You know about them?" Coulson asked. "You said something about time travelers and Russia?"

"Who were those time travelers?" Skye asked.

"The Doctor and Rose Tyler." Peggy said.

"I know them both." Jack said. "We know the Doctor many years later in the future after Rose is...gone. So what happened?"

"I traveled to Moscow with some of the Doctor's other companions last year. I won't say their names for the sake of the future." Peggy said. "We were investigating reports of disappearances at an art museum in Moscow after a new painting was put on display. When we got there, we found three Zygons, guarding the painting. They had been killing people for food."

"Were two of the Zygons named Jim and Tim?" Jack asked.

"Yes." Peggy said. "It was them and there was a female named Michelle. They were about to kill us, but then the Doctor and Rose Tyler arrived. We ran out into the street to avoid the Zygons. The Doctor used some sort of teleportation device to send a Weeping Angel to the center of the sun."

"What was a Weeping Angel doing there?" Skye asked. She was remembering the time in New York City in 2013 when she met the Doctor and Clara on her first ever S.H.I.E.L.D. mission to find and kill a Weeping Angel.

"Long story." Peggy said. "Anyway, he accidentally sent Michelle as well. Jim and Tim were going to kill us in rage. So, the Doctor used his sonic device to create a sound that only they could hear. They screamed in pain and ran off into the night. The Doctor said they would be dead soon. He then took us all home, well most of us. I lost a good friend that day. Anyway, the painting was later taken down and put into storage. Jim and Tim said that there were millions of Zygons trapped in that painting. We assumed it would just rot in storage. We thought the Zygons were dead, but you're telling me they're alive in the future."

"They are." Jack said. "They stole time energy from myself and some of the Doctor's other companions. Then, they used it to unleash their Zygon army from the painting. The last we heard was that they were invading Moscow."

"Guys." Skye said. "I have an idea. That painting is still sitting in the museum in Moscow. If we go there and destroy it. Then it won't be in tact in 2015 and the Zygons can't invade."

"That would alter the future." Thor said. "There's no telling what could happen."

"It's our best chance to save the world." Coulson said. "In 2015 the planet is attacked by Cybermen and Zygons. The human race doesn't stand a chance. But if we could remove the Zygons, we may be able to defeat Missy's Cybermen."

"That could work." Jack said. "If we destroy the painting now, then all the Zygons should disappear in the future."

"We just have to sneak into the Soviet Union." Skye said.

"I can help with that." Peggy said. "Come with me back to my apartment. I have to make some calls. We should be able to fly into Moscow tomorrow."

"Thank you Ms. Carter." Thor said. "When this is all over, I have some things to tell you about the future."

"I don't want to know." Peggy said. "It's best if I don't."

"It's about Captain America." Thor said.

Peggy froze for a moment before speaking again.

"Tell me later." Peggy said. "I can't afford to be distracted while we're saving the future from an army of Zygons."

"Fair enough." Thor said.

"Like I said, follow me." Peggy said.

Agent Carter then led Agent Coulson, Jack, Skye, and Thor through Manhattan on the way back to her apartment. Tomorrow, they would fly into Moscow on a mission to save the future. Meanwhile in 2015, Missy's army of Cybermen was beginning to clash with the Zygons and the humans.


	25. Rise of the Cybermen

Chapter 25: Rise of the Cybermen

Earth 2015

Across the planet, the strange black rain fell from the sky. It sunk into graveyards and made its way into the sewers. This was all part of Missy's plan to conquer the Earth. In every country on the planet, Cyberman began to rise from the ground. Under orders from Missy to conquer the Earth, they began attacking. The fighting was especially bad in Earth's major cities. Intense human military battles against the Cybermen erupted in Toronto, Mexico City, Rio de Janeiro, Cairo, Johannesburg, London, Paris, Madrid, Berlin, Beijing, Shanghai, Hong Kong, Tokyo, Sydney, and Mumbai. The newest Avengers (Falcon, Scarlet Witch, War Machine, and Vision) gathered in the Avengers tower in New York City after the Battle of Sokovia. They soon flew into the streets to assist the military and NYPD in fighting the Cybermen. Another hero formerly known as the Devil of Hell's Kitchen, or just simply Daredevil, also fought the Cybermen in New York. While the planet was being attacked everywhere at once, nowhere was the destruction worse than in Moscow.

* * *

Moscow, Russia 2015

Clara, Danny, Fitz, Simmons, Black Widow, and Iron Man fought valiantly with the Russian military against the Zygons. However, it seemed that the Zygon army was never ending, more and more kept erupting out of the paintings. Much of downtown Moscow was in ruins. Fires, broken glass, and dead bodies (both human and Zygon) littered the streets. The heroes knew that they could not keep this up forever. Things only got worse when the Cybermen arrived. Most people vaguely remembered the Cybermen from back in 2007, when they appeared as ghosts and then suddenly took over the planet for a few hours before the Doctor and Rose sucked them into the void at the Torchwood Tower in London. However, Clara remembered them more clearly. Before the Doctor regenerated, he took her to Hedewick's World of Wonders on a distant planet with the Maitland children. There, Clara led a small army against the Cybermen, barely making it out alive. Now, she watched in horror as they marched through the streets of Moscow in incredible numbers. They seemed to come out of nowhere. She wondered if this had anything to do with the Doctor going to wherever it is that people go when they die. Actually, Clara assumed that the two things had to be related. The Zygons saw the Cyberman army as a threat to their plans for global domination. Soon, the Zygons and Cybermen fought each other in the streets, with the humans getting caught in the crossfire. The heroes now had two enemies to fight.

* * *

3W Institute 2015

The Doctor was shocked as he stood in the hallway listening to what Missy (the Master) had to say to justify her actions. After sending Coulson, Jack, Skye, and Thor somewhere back in time, Missy told to the Doctor that she escaped from Gallifrey, which is where it always was. Now the Doctor could go and look for it. Ward, Raina, and the black Super Cyberman stood behind Missy while she told her story. Missy then professed that she made the army of Cybermen specifically for the Doctor so that he could have an army to save people across the universe. The Doctor thought her crazy and told her that he refused to accept it.

"Call off your attack!" The Doctor ordered. "You're killing millions of people just so that we could be friends again? How could you ever think I'd want to be your friend after something like that."

"I didn't do all this work for nothing." Missy said. "If you won't take charge then I will. There's a whole universe out there for me to explore and now I have a companion to do it with. I'll be just like you."

"We are not the same." The Doctor said.

"We're more alike than you care to admit." Missy said. "Now, you and I are going on a little trip."

Missy then pressed a button on her vortex manipulator. Then, both she and the Doctor became consumed by a blue light and teleported away. The Doctor suddenly found himself underground in a sewer tunnel with Missy. There was a door on the wall next to him.

"What are we doing down here?" The Doctor asked. "Where are we?"

"We're below Cardiff." Missy said.

Missy then opened the door and shoved the Doctor through it into a dark room. Then, she shut the door and locked it.

"What are you doing!" The Doctor yelled.

"I'm imprisoning you dear." Missy said. "If you're not going to be on my side, then I don't want you messing this up for me. This little prison used to belong to Torchwood. Now it's abandoned so I figured that I could use it. I used a special lock on the door. No sonic screwdriver can open it."

"I will get out of here eventually." The Doctor yelled to Missy on the other side of the door.

"I know that." Missy said. "You'll be in there long enough to be powerless to stop my conquest of this world. I've transported the TARDIS to be right above you on the surface. Let's see if you can figure out how to get to it. Goodbye for now Doctor."

Missy then teleported back to the hallway in the 3W Institute where Ward, Raina, and the Super Cyberman were standing.

"Where's the Doctor?" Ward asked.

"He's out of our way for the time being." Missy said. She then pulled out a small laser gun from her pocket and aimed it at Raina. "Say something nice."

"What?" Raina asked. "Why are you going to kill me? What about my gift? I can help you?"

"I don't want anymore spoilers." Missy said. "Where's the fun in that? Now say something nice."

"You're a bitch." Raina said.

"Thank you." Missy said.

Missy then fired a laser blast and disintegrated Raina. She would now be dead permanently.

"What do we do now?" Ward asked.

"You and I have places to go." Missy said.

"Where?" Ward asked.

"The Moon." Missy replied.

Missy then used her vortex manipulator to teleport herself, Ward, and the Super Cyberman away from 3W.


	26. Welcome Back to Russia

Chapter 26: Welcome Back to Russia

The Skies of Western Russia 1947

Coulson, Skye, Thor, and Jack awoke slowly. The last thing they remembered was drinking tea at Peggy Carter's apartment in New York City. She brought them there after promising that she'd help get them to Moscow so they could fight the Zygons. Once they destroyed the Zygon painting in the past, there would be no Zygon army trying to conquer the Earth in 2015. Now, as they gazed around it became clear that she was no longer in New York. They were sitting on a long bench. In fact they were strapped in with seat belts. They leaned back and found that there was a wall behind them. Agent Carter was sitting directly across from them. She was fully awake and also strapped to a bench with a black wall behind her. They then figured out where they were. They were on a military plane and were flying through the air. They could tell by the sudden bouncing of the plane and they could vaguely see clouds outside of the plane's few windows. It was apparently night. They must have been knocked out the entire day, or perhaps only a few hours, if they were in a different time zone.

"Sorry about knocking you all out." Peggy said. "The people flying this plane don't want anyone to know about them. We'll be flying over Moscow in a few minutes."

"You mean we'll be landing in Moscow in a few minutes." Skye said.

"No." Peggy said. "Once we're over the drop sight, they'll open the back door and we'll all jump out. There are parachutes on the floor that we'll be using."

"Who's flying the plane?" Coulson asked.

"I can't tell you that." Peggy said. "You meet a lot of people in my line of work. Not all of them want their names out there. Surely you can understand that."

"I do." He replied.

The plane's back door started to automatically open slightly.

"That's our cue." Peggy said.

Everyone then unbuckled their seat belts and carefully put on their parachutes. Thor was the only one who didn't need a parachute. When they finished, the door opened the rest of the way. Even though it was night and partially cloudy, they could see the city below them. It was the largest city in Russia and one of the largest in all of Europe. Now, Agent Carter, Agent Coulson, Jack Harkness, Skye, and Thor were about to jump into it in order to destroy the Zygons before they have a chance to destroy this city and the rest of the planet in the future. One by one, they jumped from the plane and descended into the outskirts of Moscow where no one would see them land.

* * *

Moscow, Soviet Union 1947

Peggy, Coulson, Jack, Skye, and Thor successfully landed outside Moscow unnoticed. They spent they next hour walking at night and sneaking around until they were in downtown Moscow. They were looking for The State Tretyakov Gallery, an esteemed art museum that had been reopened about a year ago. That was when Peggy was first here and fought the Zygons. The Doctor assured her that the Zygons were dead. This group from the future insisted that they weren't. In fact the two Zygons, Jim and Tim, survived long enough to unleash a Zygon army that was trapped in a painting using Time Lord technology. It was the team's mission to stop this from ever happening. No matter what happened to the timeline, it would still save millions of lives in the future.

After walking for about thirty minutes downtown, they finally found the art museum they were looking for. The building was not incredibly tall, but was still vast in size. The entrance was not particularly ornate with a simple red and white pattern on the walls and uniquely Russian architecture that made up the wooden doors, which were locked. Thor used his Asgardian strength to pull the door open without any issues. The team then walked around the halls of the dark museum for awhile until they found a door that said "basement" on it. The rest of the group could not read it, but Peggy had studied some Russian before and knew what it said. They opened the door and saw stairs leading downwards. The painting must have been kept in storage down there. Suddenly, two security guards appeared at the other end of the hall.

"Hey!" One of them yelled. This particular security guard recognized Peggy Carter.

"She's back." The other guard said. "She brought some new friends with her. What's the point in staying in these forms if she already knows we're here?"

The team only stared at the two guards, wondering if they were the two Zygons. Coulson, Skye, and Thor had never actually seen Zygons in person before. Unfortunately, they were about to. The two security guards suddenly began to morph and change. Within moments, they had transformed into tall, red aliens known as Zygons. Jack knew these Zygons as the infamous duo Jim and Tim.

"Kill them all." Jim said. "No one is getting away his time."


	27. Help

Chapter 27: Help

Cardiff, Wales 2015

The Doctor was trapped in a prison cell in the underground sewer system by Missy. The prison had once been used by Torchwood. Now that Torchwood was disbanded, the prison was abandoned, so Missy decided to use it. She put a special lock on the door so that the Doctor could not use his sonic screwdriver to unlock it. The TARDIS was parked on the street above him, but he had no way to get to it. He needed to call for help. So, he took out his cell phone and called Clara Oswald. Clara had spent most of today in Moscow. She worked with Fitz, Simmons, Danny, Black Widow, and Iron Man to stop the Zygon army from being unleashed. When that failed, they fought the Zygon army in the streets of Moscow. Things only got worse when Missy's Cybermen were thrown into the mix. After a few rings, Clara answered her phone. She was hidden inside an alleyway in Moscow so she could talk to the Doctor.

"Doctor?" Clara asked. "Where are you? There are Cybermen here too. They just appeared out of nowhere."

"There's another Time Lord here." The Doctor said. "Her name is Missy. She's crazy. She unleashed the Cybermen on Earth so she could conquer the planet before the Zygons did. There are Cybermen in every country on Earth. Also Missy is working with Ward."

"So where are you?" Clara asked.

"I'm in Cardiff." He said. "Missy put me in an underground former Torchwood prison. I can't get out. I need your help."

"I don't know what you expect me to do from Russia." Clara said.

"You need to come here and open the door." The Doctor said.

"How am I supposed to get back to Britain?" Clara asked. "By the time I get there half the planet will be destroyed."

"You know I'm good with teleports Clara." The Doctor said. "I can't use my screwdriver to open the door, but I can use it to bring you here. Just look for the TARDIS and I'll be right below it. Take the S.H.I.E.L.D. agents and Avengers with you."

"Are the others with you? Coulson? Jack? Thor?" Clara asked.

"No." The Doctor said. "I don't know where they are. I'll have to find them later. Just round up everyone and call me back. Then, I can teleport you all here."

"Then what?" Clara asked.

"Then we save the planet." The Doctor said.

* * *

Moscow, Russia 2015

Clara soon found Fitz, Simmons, Danny, Black Widow, and Iron Man amidst the chaos of the three way battle in Moscow between Cybermen, Zygons, and humans. She told them about Missy and Ward, and about the Doctor in Cardiff.

"The Doctor has a plan." Clara said. "He must. He sounded so certain on the phone. Then again, he usually just makes things up as he goes along."

"We can't save the world without him." Iron Man said. "We need to go get him."

"What about all the destruction here?" Black Widow asked.

"It's only going to get worse." Fitz said.

"We need to free the Doctor before the entire planet is destroyed." Simmons said.

"Fine." Natasha said. "Call him."

Clara then called the Doctor, who instantly picked up his cell phone. She put the Doctor on speaker.

"Is everyone there?" The Doctor asked.

"They're all here." Clara told him. "Even Danny."

"Oh great PE is here." The Doctor said sarcastically.

"This isn't the first war I've fought in." Danny said into the phone. "Like it or not you need me."

"Just do it already." Clara told the Doctor.

The Doctor then pointed his sonic screwdriver at the phone. The sonic technology then went through a complicated system of using GPS to track their coordinates. Soon, the six of them were consumed by a bright blue light and disappeared.

* * *

Cardiff, Wales 2015

Clara, Danny, Fitz, Simmons, Black Widow, and Iron Man had been teleported onto the streets of downtown Cardiff. Their goal was to find the TARDIS. Unfortunately, this would be harder than they thought. They left the Zygons behind in Moscow, but Missy's Cybermen were all over the planet, even in Cardiff. They would have to fight their way through more Cybermen. They just hoped that the Doctor could actually save the Earth when they finally did rescue him. Meanwhile in 1947, Agent Carter, Coulson, Jack, Thor, and Skye were on a mission to make sure all the Zygons in 2015 disappeared forever.


	28. Fall of the Zygons

Chapter 28: Fall of the Zygons

Moscow, Soviet Union 1947

Agent Carter, Coulson, Skye, Jack Harkness, and Thor stood in front of the entrance to the basement of the art museum. All they had to do was go downstairs and destroy a particular painting that contained millions of Zygons trapped inside. If they did that, then all the Zygons in 2015 would cease to exist. There was just one problem, well two actually. Two full grown Zygons, Jim and Tim, were preparing to attack them to prevent them from accomplishing their mission. The Zygons charged at the five of them with incredible speed. Skye stepped in front of everyone and thrusted her arms forward. As she did, Skye unleashed her inhuman powers. A sonic wave blasted out of her hands and hit the running Zygons causing them to be lifted into the air and fly backwards back where they started. Thor stepped forward with his hammer.

"Go destroy the painting." Thor said. "Skye and I can handle these two."

Peggy, Coulson, and Jack then ran down the staircase into the basement, while Skye and Thor prepared to battle the Zygons. The three of them searched through the basement. It was a series of long, dark hallways. They looked through every painting they could find until Peggy recognized the one with the Zygons in it. The painting didn't look like anything alien. It was a forest. There were no animals. Only multiple, trees and a few beams of sunlight shining through. However, there were millions of Zygons living in this forest. They needed to be destroyed in order to save the Earth in 2015. Eventually, they found it. Jack, Coulson, and Peggy took out their guns, aimed them at the painting, and opened fire. Within moments the painting was ripped apart by repeated gunfire. Now that the painting was destroyed in 1947, it would not be around in 2015 for unleashing of the Zygon army.

* * *

Moscow, Russia 2015

The city was in chaos as Cybermen and Zygons fought for control with the humans getting caught in the middle. The Cybermen had already conquered the planet. The Zygons were trying to defeat the Cybermen so they could be the masters of Earth. However, something strange started to happen. Gradually, the Zygon army, millions strong, started to fade away into nothing. Each and every Zygon that was attacking Moscow was disappearing. Agent Coulson's team went back in time and changed history. Now, these criminal Zygons never existed past 1947. All the damage they did to Moscow had been reversed. Unfortunately, Moscow was still not saved. The Cybermen caused enough destruction on their own that the city still lay in ruins. Everyone would forget that the Zygons were ever there, except for those who have ever traveled in the TARDIS. Even for just one trip. Traveling through the time vortex alters the way people see the universe. Only the criminal Zygons disappeared. There were good Zygons in London debating with Kate Stewart at U.N.I.T. about finding a new home world for the Zygons who were trapped in English paintings. Those negotiations were once again stalled to deal with the Cybermen incursion. However, there was one evil Zygon who did not disappear. Her name was Jiaying. In 1947, the Zygon who killed Jiaying and took her form was not in Moscow. So, she was not killed. Therefore, everything the Zygon Jiaying did from 1947 to 2015 was still in tact in the timeline. Afterlife, the gathering and training of Inhumans, the war with S.H.I.E.L.D., and the deadly chemicals spilled into the ocean were all still very real. Jiaying had teleported to Moscow and soon found that she was the only Zygon left fighting. The Cybermen quickly deleted her. While the world no longer had anything to fear from the Zygons, Missy's Cybermen were still brutally conquering the planet.

* * *

Moscow, Soviet Union 1947

Coulson, Peggy, and Jack returned to the upper level of the museum and found Thor and Skye standing over the dead bodies of the two Zygons Jim and Tim. They were easy for an Agardian Avenger and an Inhuman S.H.I.E.L.D. Agent to take down.

"We did it." Coulson said. "The future is safe."

"That's great." Skye said. "Now how do we get back there?"

"The Doctor will find us eventually." Jack said.

"What if Missy killed him?" Skye asked. "Even if he is still alive, he might not find us until 1982. The TARDIS isn't always accurate."

"Relax." Jack said. "We just saved the world. Have a little faith in the Doctor."

Suddenly, a blue light started to shine next to the group. Everyone then turned to look at it.

"What is that?" Thor asked.

No one knew the answer. The light then started to grow and take the shape of a human female. Jack knew what this was. It was a hologram message. He'd seen them all the time back in his home in the 51st Century. Someone was trying to contact them. Then, the features of the blue light became more distinct. Soon, a hologram of a blonde woman was standing before the group. Jack and Peggy Carter recognized this woman immediately. They were looking at a hologram of Rose Tyler.

"Rose?" Jack asked. "Is that you?"

"Yes it's me." Rose said. "Where's the Doctor? I need to speak to him. Is that Peggy Carter?"

"Hello again." Peggy said.

"He's not with us." Jack said. "How are you sending this message?"

"Believe me it's not easy." Rose said. "Sending this hologram across time and space alone was difficult. Then we tried doing across parallel worlds. Apparently it worked. We still have Torchwood on my world. They've developed some interesting technology, but never mind that. Where is the Doctor? it's imperative that I speak with him. My entire universe is in danger and unless I get his help, so will yours."

"He's not here." Jack said. "We got trapped in the past. The Doctor is still in the future."

"That makes sense." Rose said. "We sent the hologram to the last known time travel location in this universe. We assumed it would be the Doctor. Apparently it was you all instead. Who else is with you. Is that Thor?"

"Indeed." Thor said. "If you are really from another universe, then how have you heard of me?"

"My universe had our own version of the Avengers." Rose said.

"Had?" Skye asked. "Where are they now?"

"Dead." Rose said. "They died trying to fight the evil that I am now trying to warn the Doctor about."

"Don't you have a human version of the Doctor in your universe?" Jack asked.

"I don't know where he is or if he's alive." Rose said. "We were separated soon after the war broke out. Only the Doctor from your universe can help us now."

"We don't know if or when we'll see him again." Jack said. "He's in the future. Earth is being invaded by Cybermen."

"I'm dealing with something worse than Cybermen and Daleks." Rose said.

The hologram of Rose then started to flicker on and off.

"Rose." Jack said. "What's happening."

"I'm losing the connection." Rose said. "It's hard to keep it going for a long time across universes. When you see the Doctor, tell him what I'm telling you. Tell him to about the..."

Before she could finish her sentence, connection was lost. The hologram of Rose Tyler disappeared. She was trapped on her parallel world with some sort of terrible evil. It was powerful enough to destroy the Avengers. The team didn't know what to do. It seemed that all they could do was wait around for the Doctor, and they didn't want to do that in the heart of the Soviet Union. Peggy would need to get to a telephone so she could make arrangements for their travel back to the United States. Meanwhile in the future as the Cybermen conquered Earth and the Doctor was trapped below Cardiff, Missy and Ward were beginning their travels across the universe together.


	29. Missy and Ward

Chapter 29: Missy and Ward

Cardiff, Wales 2015

Clara, Danny, Fitz, Simmons, Black Widow, and Iron Man ran through the streets of Cardiff on an important mission. They had to find the TARDIS. The Doctor was put in an underground prison in the sewers directly below the big blue box. Normally, this wouldn't be a difficult mission, but Missy's Cybermen were everywhere on the planet at once, including Cardiff. Iron Man blasted Cybermen out of their way. Simmons used the laser gun she borrowed from the TARDIS to do the same. Fitz, Clara, Danny, and Black Widow followed behind. They ran through the streets for what felt like half an hour before they finally found the TARDIS. It was near the water and was parked right above where the old Torchwood Three base used to be. Apparently, now it was just a sewer. The team then ran up to the TARDIS.

"How do we get underground?" Fitz asked.

Iron Man then blasted open a nearby man hole cover that led to the sewers.

"Through there." Iron Man said.

"I'm going to stay up here." Simmons said.

"It's just a dirty sewer." Danny said.

"Well...someone's got to keep watch to make sure no Cybermen follow you down there."

"I'll do it myself." Iron Man said.

Tony then flew down into the sewer. The team then heard a small explosion come from down there. That was most likely Tony blasting open the prison door that the Doctor was in. Then, Iron Man flew back onto the street carrying the Doctor in his arms. He then let go of the Time Lord. Clara then hugged him, which made Danny uncomfortable.

"Where's Thor and everyone else?" Black Widow asked.

"Agent May, Hunter, Bobbi, Captain America, and Hawkeye are still being held prisoner in 3W. Agent Coulson, Skye, Jack, and Thor are trapped somewhere in the past." The Doctor said. "Quickly. Into the TARDIS. We've got to find the people in the past and then we'll get the group at 3W."

Everyone then ran into the TARDIS. The Doctor started maneuvering his way around the TARDIS console when he came upon something peculiar on the monitor.

"What is it?" Clara asked.

"The Zygons." The Doctor said. "They're gone."

"How can they just be gone?" Danny asked.

"Not just that." The Doctor said. "They never existed."

"I definitely remember fighting them in Moscow an hour ago." Iron Man said.

"We've all traveled through the time vortex before." The Doctor said. "It changes the way you see the universe. We can remember events that no longer happened."

"How is that possible?" Black Widow asked.

"I bet it has something to do with our friends in the past." The Doctor said. "I was right! The monitor says they're in Moscow 1947. Let's go get them."

The TARDIS then dematerialized and faded away from Cardiff

* * *

Earth's Moon 2015

In 2013, the Daleks created a large base on the moon to prepare for their attack against Earth. It was briefly visited by the Doctor, River Song, Fitz, Skye, and Thor before the Dalek attack. However, after the Dalek invasion failed, their moon base became abandoned and unused. Missy thought this was a waste. So, she decided to use it for her own purposes. Missy, Ward, and the black Super Cyberman had just teleported to this moon base from 3W. They appeared on a long metal hallway. There was a large window on one of the walls. Ward looked out and saw a black sky looming over a rocky, gray surface with many craters. He could see the Earth in the distance. Missy actually did it. She really took them to the moon.

"You built a moon base and nobody noticed?" Ward asked.

"Technically the Daleks did." Missy said. "They're not using it anymore, so I figured I'd give it whirl. Follow me."

Missy led them down more hallways. As they continued walking, Ward saw more and more Cybermen. Missy really was operating this base, but where was she bringing him? They soon came into a large room about the size of a large whale. Inside the room, was an enormous Cyber Battleship, a spaceship used by the Cybermen for war.

"How did this get here?" Ward asked.

"My boys have been busy." Missy said. "Earlier today I woke all the remaining Cybermen, but some of them were already awake. I gave them an early start so they could work on manufacturing a fleet at top speed. I have ten more ships like this one parked on the other side of the moon where no one can see them. This is how we're going to travel the universe, on a mission of conquest. My Cyberman army will conquer Earth while we search for new worlds to add to our empire."

"This is amazing." Ward said.

Missy then turned to speak to the Super Cyberman.

"I'm putting you in charge of Earth while I'm gone." Missy said. "There's a whole universe out there. I don't want to be tied down to this rock."

"Yes. Mistress." The black Cyberman said as it teleported back to Earth.

Missy and Ward then boarded the massive spacecraft. Then, they flew out of the hanger and into space. The other ten Cyber ships soon joined them. There were one million Cybermen aboard each ship. Missy was taking eleven million Cybermen with her across the universe on her mission of conquest. Missy and Ward sat in thrones on the ship's bridge as if they were the King and Queen of the universe.

"There's just one thing I want to do before we leave." Missy said. "By now the Doctor has probably broken out of the prison I left him in. Contact him!"

Within moments, a large image of the Doctor appeared on the large glass in front of them. It was this glass that separated the ship' interior from the blackness of space. Now, it was being used as a communication screen. The Doctor was currently flying through the time vortex in the TARDIS with others. They crowded into the screen as well. Fitz and Simmons were there and were horrified to see Ward sitting comfortably next to Missy.

"What do you want?" The Doctor asked.

"I'm just letting you know that I'm leaving." Missy said. "My boys have already taken over the Earth. The Zygon threat is gone. It's time to move on. Goodbye for now, Doctor."

Missy then hung up on the TARDIS. The screen went away and returned to normal glass that the pilots could see out of to fly the ship.

"So where are we going again?" Ward asked.

"Asgard." Missy said. "I want to visit a friend there before the Cybermen conquer that world as well."

"What friend?" Ward asked.

"He is known throughout the universe by many names." Missy said. "You probably know him as Loki."

Missy's eleven spaceships and eleven million Cybermen then prepared to leave the moon. On Missy's command, the Cyberships sped away from planet Earth on their way across the stars, leaving Earth to fall to the Cybermen that were already there.


	30. The Plan

Chapter 30: The Plan

Moscow, Soviet Union 1947

Agent Carter, Agent Coulson, Jack Harkness, Skye, and Thor stood inside an art museum in downtown Moscow. They'd just destroyed a painting in the basement that contained millions of Zygons, thus preventing the Zygon Invasion in 2015. The museum was closed and it was night. They didn't know if or when the Doctor would come to bring them back to the future. They'd just talked to a hologram of Rose Tyler, who warned them of an unspeakable evil that was threatening her universe. Her version of the Avengers died fighting it. The connection was lost before she could tell them the name of the evil. The five of them tried to figure out what to do next. Suddenly, there was a strange wind inside the museum followed by a loud wheezing sound. Everyone recognized it as the sound of the TARDIS. The blue box soon materialized mere yards away from the group. Then, the doors opened and out stepped the Doctor, Clara, Danny Pink, Fitz, Simmons, Black Widow, and Iron Man. This was Simmons', Natasha's, and Tony's first time travel adventure. The Doctor looked different than how Peggy remembered him. She assumed he must have aged.

"What have you all done?" The Doctor asked. "In the future, the Zygons are gone. Well more than that, they never even existed."

"We destroyed the painting now, so that it couldn't be opened in the future." Coulson said. "Is the world safe now?"

"No." Clara said. "Missy's Cybermen are still everywhere."

"Missy and Ward also left." Simmons said. "They're going to conquer other planets too."

"We should focus on saving our own planet first." Iron Man said.

"How?" Skye asked. "It's not like we can blow them all up. We sent all Earth's nuclear missiles to destroy the Dalek fleet in 2013."

"There are billions of Cybermen all over the planet." Black Widow said. "We need a way to destroy all of them at once."

"That's impossible." Danny said.

"No it's not." The Doctor said. "We just have to open the Cardiff Rift."

"The what?" Clara asked.

"There's a space-time rift that runs right through Cardiff." The Doctor said. "I can use the TARDIS to open it and calibrate it so that only Cybermen will get sucked into it."

"Where will they go after they get sucked through?" Fitz asked.

"They should end up somewhere in space, but they'll be broken beyond repair by the intensity of traveling through the Rift." The Doctor said.

"Doctor." Jack said. "There's something else. We just talked to a hologram from the future...and from another universe."

"That's impossible." The Doctor said.

"The hologram was Rose." Jack said. "She's back on her parallel Earth. She said her entire universe is in danger and that if we don't help her, our universe will be in peril too."

"Our universe is in peril now." The Doctor said. "What's so terrible that she had to break through the walls of universes to send this message?"

"We don't know." Thor said. "The connection was lost before she could give its name."

"Then it can wait until after we stop the Cybermen." The Doctor said. "Now, everyone in the TARDIS. We need to get back to the future and rescue the others."

"Doctor." Peggy Carter said. "You're so much older than the last time I saw you. You may not remember me. I'm Agent Peggy Carter. My place is here, in 1947. I wish you the best of luck in 2015, but I need to stay here. Would you mind dropping me back off in New York City before you fly to the future?"

"Of course I remember you." The Doctor said. "Get in the TARDIS. We'll give you a ride."

Then, everyone piled back into the TARDIS, which had beyond enough space to carry the large group. The TARDIS made a brief stop in Manhattan 1947 to allow Peggy to leave before the box faded away again on its way to the future. As Peggy walked home, she realized that she never heard about Steve. Thor had something he wanted to tell her about Captain America, but he never got around to it. She supposed it was probably for the best anyway and kept walking. Meanwhile in 2015, planet Earth was now at the mercy of the Cybermen.


	31. The Super Cyberman

Chapter 31: The Super Cyberman

3W Institute 2015

The TARDIS materialized inside the hallway of the 3W Institute where Captain America, Hawkeye, Agent May, Hunter, and Bobbi were all unconscious and being held captive inside the empty tanks that used to hold the Cybermen. Before they stepped outside the blue box, the Doctor had a warning to give everyone.

"Before you go outside, there's something you need to know." The Doctor said. "Missy has a Super Cyberman."

"What's so super about it?" Clara asked.

"It can scan people and copy their abilities." Jack said.

"It's true." Thor said. "It scanned me. Then, when I tried to through my hammer at it, the Cyberman caught it and threw it back. As you know, Vision and I are the only ones who can lift the hammer."

"It copied my powers too." Skye said.

"It's also has Captain America's fighting skills and Hawkeye's accuracy." The Doctor said.

"Let's be glad the Hulk isn't here." Iron Man said. "I'd hate to see what this Cyberman could do with his powers."

"What does it look like?" Danny asked.

"It looks like a normal Cyberman." Coulson said. "However, it is painted black instead of silver. You can't miss it."

"If we hurry, maybe we won't even see it." Simmons said.

The large group of them then exited the TARDIS and walked down the hall. They saw their comrades unconscious and strapped to chairs behind the glass on the wall in tanks.

"How do we wake them up?" Fitz asked.

The Doctor then whipped out his sonic screwdriver and activated it. Then, all the glass in the room shattered and the five prisoner woke up.

"What's happening?" Hunter asked.

"Where are we?" Captain America asked.

"Long story." Black Widow said.

"We need to get back to the TARDIS now." The Doctor said.

"Halt!" A strange voice yelled from the other side of the hall. Everyone turned to see the black Super Cyberman standing there. "You will not leave. The Mistress has left the planet. I am in charge while she is away. Do as I say."

Iron Man then flew above the group, extended his arms towards the Cyberman, and sent powerful laser blasts at it. The Cyberman used Captain America's speed to jump out of the way in time. As it did, it scanned Iron Man, and copied his abilities. Tony Stark's lasers were more powerful than a regular Cyberman's lasers. The Cyberman then used its feet as small rockets to propel itself into the air, just as Iron Man was doing. Then, the Cyberman thrusted its arms forward, using Skye's powers to create a sonic blast that sent Iron Man flying all the way to the other side of the room where the TARDIS was parked. Fortunately, the rest of the team had already hurried inside the TARDIS while Tony distracted the Cyberman. So, Iron Man rushed inside as well. The TARDIS soon faded away.

As the Doctor flew his time machine through the time vortex, the others filled Captain America, Hawkeye, May, Hunter, and Bobbi in on what had happened. They told them that the Doctor was planning to open the Cardiff Rift and calibrate the TARDIS so that only the Cybermen would be pulled inside. They would most likely end up damaged and destroyed at the other end of the universe,though there was a small chance they would emerge onto another world somewhere. The Super Cyberman watched as the TARDIS disappeared. The Cyberman used its incredible wealth of knowledge and mathematics to calculate the most likely plan that the Doctor and his friends came up with to stop Missy's Cybermen. It concluded that they would attempt it open the Cardiff Rift and suck in the Cybermen. So, the Super Cyberman ordered more units to be sent to Cardiff to protect it and stop the Doctor, the S.H.I.E.L.D. agents, and the Avengers.


	32. The Final Battle part 1

Chapter 32: The Final Battle part 1

The TARDIS raced through the time vortex as it normally did while in flight. However, there were far more passengers standing in the TARDIS console room than normal. In addition to the Doctor and his regular companion Clara Oswald and her boyfriend Danny Pink, the TARDIS was also carrying the Doctor's former companion and former head of the Torchwood Institute, Captain Jack Harkness. Agent Coulson, the head of S.H.I.E.L.D., was also there with his S.H.I.E.L.D. team consisting of Agent May, Skye, Fitz, Simmons, Hunter, and Bobbi. Most of the Avengers were also there, including Iron Man, Captain America, Black Widow, Hawkeye, and Thor. They were all heading to Earth for one last stand against Missy's Cybermen. The rest of the Avengers were already fighting the Cybermen from the Avengers Tower in New York City. Missy and Ward left the planet with eleven Cyberships to conquer other worlds. Planet Earth was occupied by the Cybermen in her absence.

The Doctor's plan was simple enough. There is a space-time rift that runs through the city of Cardiff. The rift acted as a gateway to other worlds and time periods. Occasionally, aliens or other supernatural objects would appear through this invisible rift and land in Cardiff. The Torchwood Institute used to monitor the rift before it was disbanded. They would deal with these alien events. Since Torchwood ceased to exist back in 2009, U.N.I.T. has been watching the rift. However, U.N.I.T. was busy dealing with the Cyberman Incursion. The Doctor planned to use the TARDIS to open the Cardiff Rift, thus opening a portal to another random world. He would then use the science of the TARDIS and the power of the Rift to suck in all the Cybermen across the globe. They would be so damaged from the journey that they would be destroyed in whatever world they went to. Only the Cybermen would be sucked into the Rift. Humans, animals, and inanimate objects would be unaffected. However, the Cybermen would not go down without a fight. Missy left a black Super Cyberman in charge of Earth and it knew what the Doctor was planning. The Super Cyberman had all the powers of the Avengers and would be a challenge to defeat.

"The Cybermen know we're coming." The Doctor said. "I hate to ask this of you all, but I need to stay in here and open the Rift. The TARDIS needs to be defended."

"Say no more." Phil Coulson said as he took out his gun.

"We'll gladly fight if it means saving the world." May said.

"Be careful of the Super Cyberman." The Doctor warned. "It has all of your strengths and will be much harder to destroy than the other Cybermen."

"How long will it take for you to open the Rift?" Bobbi asked.

"About ten minutes." The Doctor said. "Believe me, that's as fast as its gets. It would normally take hours to open a rift in time and space."

"Then why is it only going to take ten minutes?" Captain America asked.

"Because I'm using the TARDIS." The Doctor replied.

* * *

Cardiff, Wales 2015

The TARDIS materialized in downtown Cardiff above where the old Torchwood base used to be by the water. There were Cybermen all over the city. They knew what the Doctor was planning and they were ready to fight him. This was planet Earth's last hope. Soon, the TARDIS doors opened and the Avengers practically flew out into the city. The black Super Cyberman was flying in the air, while the other Cybermen were on the streets. Iron Man and Thor flew up high to fight the Super Cybermen while the others used their weapons and their skills to attack the other Cybermen that surrounded the TARDIS. However, they were not alone. Agent Coulson and his experienced S.H.I.E.L.D. team soon ran out of the TARDIS with their own weapons to help the Avengers defend the TARDIS. Skye used her powers to create sonic blasts that blew away dozens of Cybermen at once. The Doctor, Clara, Danny, and Jack remained inside the TARDIS.

"I need absolute concentration." The Doctor said as he raced around the TARDIS console pressing all sorts of buttons and pulling levers all over the place.

"We should go outside and help." Jack said.

"Stay here." Danny said to Clara.

"No way." Clara said. "I'm not leaving you. Besides I fought the Cybermen and the Zygons with you back in Russia."

Jack had an extra laser gun that he picked up in the seldom used TARDIS armory while they were flying to Cardiff. He gave it to Clara and then walked outside to join the fight.

"Stay close to me." Danny said. "We'll get through this together."

Clara and Danny then walked over to the TARDIS doors. Clara turned around to look at the Doctor, who was purposely avoiding her glance. Then, the two of them walked outside to help fight the Cybermen. The Doctor remained inside the TARDIS alone. He could hear the sounds of lasers, explosions, and screams coming from outside. He didn't want any of this to happen. Why had the Master been so crazy? He blamed Missy for this. He blamed Missy for the fact that all his friends were out there fighting to protect him while he opened the rift. He started to wonder about his old companion Rose Tyler. Jack received a hologram message from Rose saying that her universe was in danger and that they needed the Doctor. He knew he'd have to figure that mess out once this one was over. He also thought about Clara. It was likely that if Danny and Clara survived this, that they would want to start a life together. That meant Clara would stop traveling in the TARDIS. He wasn't sure he could handle that yet. It was like he constantly had more and more problems. The Doctor became consumed by his thoughts and almost didn't notice that he was receiving an incoming message. The Time Lord walked over to the screen and saw Missy and Ward sitting down in their Cybership as it traveled across the universe.

"What do you two want now?" The Doctor asked.

"Just checking in on Earth." Missy said. "How's my new planet doing?"

"It won't be yours for much longer." The Doctor said.

"We'll see about that." Missy said. "I just wanted to let you know that I'm preparing to invade the next planet on my list to add to my empire. I figured you should know. It's only fair."

"What world are you talking about?" The Doctor asked.

"Asgard." Missy replied.

The image of Missy and Ward soon disappeared. She had ended the message. That was just another problem the Doctor would have to deal with. However, none of it would even matter if the Avengers, S.H.I.E.L.D. agents, and companions couldn't protect the TARDIS. None of it would matter if the Doctor couldn't open the Rift.


	33. Meanwhile on Asgard

Chapter 33: Meanwhile on Asgard

Missy, Ward, and their eleven Cyberships traveled at hyper speed across space until they stopped above a sparkling world similar to Earth. This world was Asgard. The spaceships hovered in the stars above.

"Shall we begin the attack?" The Cyberman piloting the mothership asked Missy, who was sitting on the bridge with Ward in chairs that resembled royal thtones.

"No." Missy said. "I need to talk to the King first."

* * *

Asgard 2015

It seemed that the world of Asgard was constantly under attack during the last few years. In 2011, a group of Frost Giants were let into the royal castle by Loki and attempted to kill King Odin after Loki usurped the throne and sent the Destroyer to Earth to kill Thor in New Mexico. Fortunately, the Frost Giants failed and Odin was restored to the throne. In 2012, Loki teamed up with the Chitauri to invade New York City as part of their plans to conquer the Earth. He was defeated by the Avengers, including Thor and brought back to Asgard, where he was imprisoned. In 2013, the Doctor and River Song arrived in Asgard and assisted Thor, Lady Sif, and the Warriors Three in defeating the enchantress Lorelei. Also in 2013, Loki was released to assist Thor in defeating the Dark Elves, who also attacked Asgard. While Thor was on Earth fighting Malekith and the Dark Elves in London, Loki again usurped the throne of Asgard. However, only he was aware of this. Loki used special power to take the form of King Odin. Everyone believed he was the real king. No one, not even Thor, suspected that Odin was really Loki in disguise. Now, in 2015, Asgard was again in danger. This time, it was from the Cybermen. King Odin (Loki) was sitting in his royal throne, when suddenly a royal guard came in and ran up to him.

"My King." The guard said. "There have been ships spotted in the sky. We believe that they mean to attack Asgard."

"Where are they from?" Odin asked.

"We don't know." The guard said. "We've never seen them before."

Suddenly, a large flash of blue light appeared in the center of the room. When the light disappeared, Missy, Ward, and two Cybermen were standing there. The royal guards in the throne room aimed their spears at the intruders and prepared to fight.

"Who are you?" Odin asked. "Who dares attempt to attack my world?"

"You don't remember me?" Missy asked. "I suppose I have changed a bit since we last met. I go by Missy now, but back in the day, people called me the Master."

"Guards." Odin said. "Leave. Allow me to speak privately with our visitors."

Just as the King commanded, the guards soon left the room.

"You can cut the charade now." Missy said. "I know it's you Loki."

A strange light then consumed Odin and he was turned into Loki.

"Tell me who you really are." Loki said. "I've revealed my true self to you. You cannot possibly be the Master. The Master is not a woman."

"She is now." Missy said. "I told you about the regeneration process when we spoke last. You do remember Harold Saxon don't you?"

"How could I forget?" Loki asked. "I suppose it is you after all."

"Would you mind explaining?" Ward asked Missy.

"Back when I had a different face and became trapped in the Time War with Rassilon and the other Time Lords, I reached out for help. The only one who answered was Loki. We had such grand plans, but he decided to align himself with the Frost Giants and then the Chitauri and forget about me." Missy said.

"Look where it's gotten me." Loki said. "I regret nothing. Is that why you've come with your metal men? You want to attack Asgard as revenge for how I left you?"

"My Cybermen have already conquered Earth." Missy said. "As I recall, that was your mission, but you failed. What's to stop me from conquering this world? As more Asgardians die, they will become Cybermen. My army is endless."

Loki had to pause for a moment and consider Missy's words.

"What if I propose an alliance?" Loki asked.

"What would an alliance with Asgard do for me?" Missy asked. "I could just control Asgard instead of working with it."

"Asgardians are powerful." Loki said. "If you kill us all, you lose that power. If you align with us, our power becomes yours and this beautiful world doesn't have to be destroyed."

"I suppose you make an excellent point." Missy said. "I'll take you up on that offer. There will come a day when I call upon the power of the Asgardians. If they do not come to me, then my Cybermen will destroy this world Loki. I promise you that."

Missy, Ward, and the Cybermen then teleported back to their spaceship that was hovering above the planet with ten other Cyber war ships.

"What do we do now?" Ward asked.

"We move forward." Missy said. "We will conquer Asgard someday, but not today. I'm sure we can use the Asgardians to our advantage in the future. We're going across the galaxy to the next planet."

"What planet is that?" Ward asked.

"Xandar." Missy said.


	34. The Final Battle part 2

Chapter 34: The Final Battle part 2

Cardiff, Wales 2015

Battles raged across the world as the Cybermen conquered the planet and began converting innocent humans into Cybermen. The most intense battles were in New York City and Cardiff. In New York, a faction of the Avengers (War Machine, Scarlet Witch, Falcon, and Vision) fought the Cybermen with the N.Y.P.D. and U.S. Army. Another hero fought the Cybermen as well, but remained largely in the Hell's Kitchen section of Manhattan. He had gained fame as the Devil of Hell's Kitchen for stopping the sinister Wilson Fisk earlier in 2015. Now, people knew him as the Daredevil. Across the pond in Britain, the Cybermen focused an intense effort on Cardiff. It was here that the Doctor planned to use the TARDIS to open a space-time rift through the city that would suck in all the billions of Cybermen across the planet. The Cybermen were determined to prevent this.

Leading the fight was Missy's black Super Cyberman that had all the powers of the Avengers and Skye. Thor and Iron Man fought the Super Cyberman as they all flew through the air above the city. Iron Man would fire lasers at it and Thor would send lightning towards it. However, the Super Cyberman had the skill to avoid these attacks and send back its own lasers and lightning. It was a truly formidable adversary. The rest of the team fought the Cybermen on the ground. They surrounded the TARDIS, preventing the Cybermen from getting to it. Captain America, Hawkeye, and Black Widow were the three Avengers on the ground. They were assisted by Phil Coulson's S.H.I.E.L.D. team as well as Jack Harkness, Danny Pink, and Clara Oswald. They held special laser guns that could destroy Cybermen. While they fought valiantly, they could not do it forever. The Doctor still needed time in the TARDIS to open the rift.

Captain America, Black Widow, and Hawkeye felt a sense of déjà vu. They had fought Ultron's robots in Sokovia yesterday and today, they were fighting more robotic men. After this fight, assuming they saved the planet, Hawkeye would retire from the team, at least temporarily, to be with his wife. They were expecting their third child very soon. As more and more Cybermen appeared, the battle became more intense. Skye used her new powers to create sonic blasts that wiped out entire groups of Cybermen at once. Everyone felt lucky that she was on their side. Danny and Clara stood side by side shooting Cybermen from every angle. They were the perfect duo. Fitz and Simmons also employed this strategy. Jack and Agent May worked together, just as they had done in New York against the Daleks and Chitauri back in 2013. They also made a good team. Coulson stayed with Hunter and Bobbi. The three of them were excellent fighters and shooters. Despite their efforts, more Cybermen kept coming. The Doctor needed to do something soon. Inside the TARDIS, the Doctor was almost ready to open the rift. He'd spent ten minutes maneuvering around the TARDIS console, gathering the power within the TARDIS to perform such a feat. Now, it was time. He calibrated the TARDIS so that once the rift was opened, only the Cybermen would be lifted into the air and sucked into the rift. Humans, animals, and inanimate objects would be unaffected. Then, the Doctor pulled down hard on one last lever.

The battle continued in Cardiff until something strange happened. It happened in the sky above the city. What looked like a bolt of lightning ran straight across the sky over Cardiff. The Doctor ran outside to see it. He thought it looked similar to the cracks in the universe that he encountered in his eleventh incarnation. Then, this crack across the sky started to open. Inside the crack, there was only darkness and black. Suddenly, all the Cybermen on the ground started to be lifted into the air and then flew right up into the Cardiff Rift that had now been opened across the sky. The Super Cyberman was sucked inside as well. Thor and Iron Man landed on the ground to avoid the massive flooding of Cybermen through the air and into the rift.

This phenomenon occurred all over the world. Cybermen in the United States, Canada, Latin America, Europe, Africa, Asia, Oceania, and even Antarctica were lifted into the air and flown across the planet towards Britain to be sucked into the Cardiff Rift. Once through the Rift, the Cybermen would travel to a random new world. However, by the time they got there, they would be destroyed from the intense journey through the rift. The Cybermen would not be able to harm any life that existed on the new random world they were headed to.

It only took thirty minutes. The Doctor, his companions, the S.H.I.E.L.D. team and the Avengers stood on the street in Cardiff next to the TARDIS and watched for thirty minutes as billions of Cybermen from across the planet were sucked into the Cardiff Rift at massive speeds. When the last Cyberman was consumed into the rift, every person in every country celebrated the liberation of the planet. However, the Rift was still open.

"We did it!" Hunter shouted.

"Congratulations everyone." Coulson said. "A very special thanks to the Doctor."

"Are you going to close the Rift now?" Clara asked.

"I programmed the TARDIS to close the Rift once all the Cybermen were sucked in." The Doctor said. "It would only stay open like this if...oh no."

"What?" May asked. "What's the problem now?"

"The rift is a gateway to other worlds and time periods." The Doctor said. "We sent the Cybermen through to another world. That world is sending something back. The rift will stay open until whatever that world is sending comes through."

"It could be a gift." Iron Man said.

"It could be a galactic army." Captain America said.

"We could be facing another invasion?" Fitz asked.

"We're about to find out." Simmons said.

The group stared upwards at the blackness of the open rift, waiting for something to come out. Eventually something did fall out. It wasn't an army of spaceships or an asteroid. Instead, it was a woman. A blonde woman had just come out of the rift. However, she wasn't flying. She was falling. The blonde woman was falling helplessly from the rift high in the sky towards Cardiff. Thor immediately flew upwards to rescue her. He caught the blonde woman in his arms in mid air and brought her back down to the group. She then stood on her feet to address everyone.

"That's impossible." The Doctor said. "You can't be here."

The blonde woman who fell through the rift and was now standing in front of everyone was the one and only Rose Tyler. She came to warn them all of the evil that had already ravaged her universe. It was a new race of powerful monsters called the Cyber-Daleks.


	35. The Cyber-Daleks

Chapter 35: The Cyber-Daleks

Cardiff, Wales 2015

Once again, the Doctor, the S.H.I.E.L.D. team and the Avengers had saved the Earth. Every single one of Missy's Cybermen on Earth had been completely sucked into the Cardiff Rift that opened in the sky above the city. However, something came out of the rift as well. The Doctor's old companion Rose Tyler fell out of the rift and was saved by Thor. Then, the Cardiff Rift closed and the sky above Cardiff returned to normal. Everyone was perplexed by Rose's arrival, especially the Doctor. Her hair was still blonde, but longer than he remembered. She wore a black leather jacket, black pants, and black boots. She stood in front of the Doctor, Clara, Danny, Jack, Phil Coulson and his team, and the Avengers on the street next to the TARDIS.

"That's impossible." The Doctor said. "You can't be here."

"Doctor?" Rose asked. "Is that you? Have you regenerated again?"

"Twice." The Doctor said. "Rose. I don't understand. How did you come through the rift?"

"It's a long story." Rose replied. "I sent a message to Jack. He said this world was being invaded by Cybermen."

"It was." The Doctor said. "We stopped it."

"Will someone please explain what's happening?" Hawkeye asked.

"This is Rose Tyler." The Doctor said. "We used to travel together. Now she lives in a parallel universe. Travel between parallel worlds is supposed to be impossible, which is why I'm so surprised to see her here."

"I wish we had time to reminisce, but that's not why I came back." Rose said. "I need your help."

"Of course you do." The Doctor said. "Jack tells me your universe is fighting an unspeakable evil."

"Yes." Rose said. "My parallel Earth is at war. By now they've probably spread to other planets too. They killed my world's version of the Avengers. Your human clone and I got separated about a year ago and I haven't heard from him since. I fear that he may be dead. Torchwood is the dominant global intelligence agency on my world. We put both S.H.I.E.L.D. and H.Y.D.R.A. out of business years ago. I became the head of Torchwood after a few years. This whole thing is on me for not doing enough to stop it earlier. I'm sorry I had to come here and beg for help, but I have no other options."

"What evil are you talking about?" Coulson asked. "Tell us the whole story."

"The evil I'm talking about is a new race of killer aliens called the Cyber-Daleks." Rose said. "They were created in my universe by Tony Stark."

* * *

The year was 2012. In this parallel world, the Avengers were assembled by the Torchwood Institute, run by Rose Tyler, to combat an invasion of the planet by the Sontarans. The Avengers defeated the Sontarans and sent them back into space. This world's version of Iron Man was worried that if Earth ever came under attack again, that the Avengers might not be enough to stop it. So, he created a weapon that would be able to defend the Earth if the Avengers could not. A version of Cybermen originated on this world and terrorized it when the Doctor and Rose first came to the parallel world. Stark was easily able to get the blueprints to construct a Cyberman. However, he wanted it to be upgraded so that it would be able to be unstoppable. So, Tony Stark stole classified blueprints for Daleks from Torchwood. He made an indestructible hybrid of the two aliens called a Cyber-Dalek. It looked like a shiny, silver Dalek. However, it was more powerful than any normal Dalek. It's goal was not mindless extermination. It's goal was to fight the enemy and convert them into more Cyber-Daleks so that Earth would eventually have its own army of them. Rose was against the Cyber-Dalek model from the start, but it did prove effective in defending the Earth against an asteroid and a small invasion attempt by the Silurians. So, she allowed the program to continue under a watchful eye.

Eventually, this single Cyber-Dalek realized that it was more powerful than any human and was therefore superior, a mentality shared by both the Daleks and the Cybermen. Tony kept his creation in his laboratory in his home in Malibu. One night, the Cyber-Dalek broke out of its cage and killed Tony Stark and his wife Pepper Potts. Once dead, it used their brains for another purpose, to live again as Cyber-Daleks. They had been converted. Soon, the three Cyber-Daleks went on secret missions to find people across the world and convert them into Cyber-Daleks. Rose was unaware this was happening. This continued for another two years until finally, the Cyber-Daleks had grown to be in the millions. So, they launched a surprise attack on the parallel Earth in 2014. Torchwood scrambled to find weapons at its bases across the globe to help fight the Cyber-Daleks, but none of their weapons were successful. Rose became separated from her family and the human Doctor when Cyber-Daleks invaded their home in London. Rose was forced to remain in the city and command the Torchwood Army against the Cyber-Daleks. She sent her family and the human Doctor to rural Scotland, where she hoped they'd be safe.

Rose continued to fight the Cyber-Daleks with Torchwood for a year before it became clear that the human race had lost. Rose returned to her office at Canary Wharf in London in 2015, one of the only skyscrapers left standing in the entire city. She was hoping to find something in the secret alien vaults that could help them, but all she could find was a powerful alien device capable of projecting a hologram across time and space and universes. She thought this would be the way to contact the Time Lord Doctor back in her native universe and ask for help. Unfortunately, she wasn't able to talk to the Doctor. She spoke to her old friend Jack Harkness for a few minutes before the connection was lost. Rose had to sneak around. The building had been abandoned when London was conquered by the Cyber-Daleks. The Avengers had tried to fight these monsters, but they all perished in battle. Rose sat in her old office, trying to think of what to do next. She looked down out the window at the destruction. London, like so many other cities on this parallel world, had become a battleground. Unfortunately, Rose had stayed in the building too long and was spotted by the Cyber-Daleks. Suddenly, her door was busted open by a Cyber-Dalek laser blast. The silver creature made its way closer into the office.

"You will be upgraded." It said with the voice of a Cyberman.

"Never." Rose said.

"Then you will be exterminated." The Cyber-Dalek said.

Suddenly, a strange event was occurring outside that made both Rose and the Cyber-Dalek look out the window. What looked like a bolt of lightning ran straight across the street next to the skyscraper that Rose was in. It looked similar to the cracks in the universe that the Doctor encountered in his eleventh incarnation. Then, this crack across the street started to open. Inside the crack, there was only darkness and blackness. Then, billions of pieces of broken Cybermen erupted out of this rift in the ground and littered the streets. Rose saw this as her opportunity to escape. These Cybermen came from somewhere. The hologram she spoke to of Jack Harkness said that their Earth was being invaded by Cybermen. If these were those Cybermen then that Earth was now safe and the Doctor could help her. Rose wasted no more time. She jumped out the window and let herself fall through the air until she fell through the rift in the ground and reappeared in Cardiff in her original universe in the air. The rift then closed, trapping Rose in this universe while the Cyber-Daleks continued to destroy the other one.


	36. Warning

Chapter 36: Warning

Cardiff, Wales 2015

Rose finished telling her story about the creation and spread of the Cyber-Daleks across her parallel Earth to the Doctor, Clara, Danny, Jack, Coulson's team, and the Avengers.

"I need your help Doctor." Rose said. "I left my universe behind, but I want to go back someday and destroy the Cyber-Daleks. Will you help me figure out how to do that?"

The Doctor paused for a moment. It seemed there was just one problem after another that he needed to deal with. Missy and Ward were somewhere out in the universe using an army of Cybermen to conquer other worlds. Now, Rose traveled across universes just to find him and ask for help. He couldn't quite say no.

"Sure I will." The Doctor said. "Let's get everyone back home first."

"There's something else you should know." Rose said. "The rift opened in my universe and the broken Cybermen came out. I jumped through it and landed here. The Cyber-Daleks will likely scan the broken Cybermen and determine that they came from this world."

"So what?" Iron Man asked. "It's not like they can travel across parallel universes by themselves."

"That's the thing." Rose said. "My world's version of Iron Man created the Cyber-Daleks to be fiercely intelligent. They have the combined intelligence of a Dalek and a Cyberman. Now that they know there is a whole other universe for them to conquer, they will try to do it. They'll work endlessly to figure out a way to travel across parallel worlds. I mean that literally. Those machines don't sleep. You can be sure that they will make their way over to this universe some day. It's only a matter of time."

"The universe is so vast." The Doctor said. "Surely there's something out there that can get you back home and defeat the Cyber-Daleks before they come here. We just have to find it. You'll join me and Clara in the TARDIS and we'll start searching."

"Who's Clara?" Rose asked.

"That's me." Clara said as she stepped forward and shook Rose's hand. "I've been traveling with the Doctor most recently."

"It's a pleasure to meet you." Rose said.

"Well..." Fitz said. "Even though that's terrible and will surely be a problem one day, let's not forget that we just saved the planet from Cyberman and Zygon invasions."

"Fitz is right." Coulson said. "Let's focus on that right now. We should all celebrate."

"Let's all go back to the Avengers Tower in New York." Black Widow said. "We can have a little party."

Everyone was in unanimous agreement about the party. The large group then entered the TARDIS. Soon, the box dematerialized. As the TARDIS flew through the time vortex on its way to New York City, Rose couldn't help but feel that a party was the wrong thing to do. Her planet was suffering. Her entire universe was now in danger. She wasn't wrong about the Cyber-Daleks. One day, they would figure out a way to travel across parallel universes and invade planet Earth.


	37. Thanos

Chapter 37: Thanos

Xandar 2015

After some more time traveling at high speed, Missy's eleven Cyber-ships flew above the Earth-like planet of Xandar. Xandar is the capital of the Nova Empire, a series of planets across this particular galaxy. In 2014, the Xandarian war against the Kree Empire briefly started up again. Ronan the Accuser used the power stone, one the six powerful infinity stones, and almost destroyed the planet. However, he was stopped by the Guardians of the Galaxy led by Peter Quill, also known as Star Lord. The power stone, known locally as the Orb, was then kept in the capital. Now, the planet was once again under attack. Innocent humans, humanoid aliens, robots, and other creatures inhabited Xandar. They all became frightened when they looked up at the sky and saw strange metal men flying around the blue sky and firing lasers down on them. Missy had sent her Cybermen down to Xandar to conquer this world to add to her own new empire. Irani Rael, a tall, experienced woman who was also the leader of the Nova Empire and its military the Nova Core, immediately called a meeting of her advisors in the great hall of the capital.

"What are these metal men that are attacking us?" She asked.

"I have heard legends that speak of such things." One of her advisors said. "In myths, they are called Cybermen and they are deadly."

"Then we fight back." Irani declared. "We're going to give them everything we've got and quickly. Their attack has already begun. Call the Guardians of the Galaxy. We may need their help again. Above all else, make sure the Orb is protected."

While the Cybermen began their conquest of Xandar, Missy and Ward remained on the mothership hovering above the planet.

"Mistress." One of the Cybermen on board the ship said. "The Earth is no longer ours."

"What!" Missy yelled.

"Every Cyberman on Earth has been deleted." The Cyberman said.

"How did he do it?" Ward asked. "How could the Doctor pull that off?"

"I don't know." Missy said. "Well, I have new plans for Earth anyway."

"What plans?" Ward asked.

"If I can't have the old Earth, I'll just have to make a new one." Missy said.

What happened next was sudden and strange. Missy and Ward were looking at each other. When they turned to look back at the Cyberman, they found that he was gone. They found that their entire ship was gone. Xandar was gone. They had apparently moved. Missy and Ward were somehow teleported somewhere else. Missy and Ward now found themselves outside. They stood on a gray, rocky ground similar to Earth's moon. When they looked up, they found that they were in space. There were numerous large chunks of rocks floating amongst the stars above them. Hovering just above them was a large man in a special throne. This man had a purple face and power hungry eyes. His name was Thanos.

"I have brought you here." He said. "I am Thanos."

"Am I supposed to believe that?" Missy asked. "Thanos is just a myth."

"The Doctor and the Master exist in stories, but are truly real." Thanos said. "You will find that I am no different."

"I don't understand." Ward said.

"Just let me do the talking." Missy said. "Why have you brought us here?"

"You're on a path of domination." Thanos said. "You caught my attention when you entered this galaxy. You are currently invading Xandar. There is a special stone on that planet and five others like it across the universe. I want you to collect those stones and give them to me. In return I will allow you to conquer as much of the universe as you please."

"You will allow me?" Missy said with a chuckle. "I'm doing just fine on my own."

"Because I allow it." Thanos said. "I am more powerful than you. Do not test me."

"Fine." Missy said. "If it will shut you up and bring me back to my ship then sure. I'll get the stones for you. Where are they?"

"When the time comes, you will know." Thanos said.

In the blink of an eye, Missy and Ward found themselves back on the Cybership hovering above the planet Xandar.

"What just happened?" Ward asked.

"Just another thing to add to my to-do list." Missy said.

* * *

New York City, United States 2015

The TARDIS materialized at the Avengers Tower in Manhattan. Before exiting the TARDIS, the S.H.I.E.L.D. team and the Avengers once again thanked the Doctor and his companions for helping them fight for the Earth and save it from multiple alien menaces. Then, Agents Coulson, May, Fitz, Simmons, Skye, Hunter, Bobbi, Iron Man, Thor, Captain America, Black Widow, and Hawkeye all stepped out to have a celebration of their triumph. They were greeted by Maria Hill, Pepper Potts, War Machine, Falcon, Scarlet Witch, and Vision. The Doctor and his companions then joined the party for a few hours before finally bidding farewell to their friends and flying away in the famous blue box. Inside the TARDIS was the Doctor, Clara, Danny, Jack, and Rose. They were about to decide what to do next, when suddenly, Martha Jones and Mickey Smith entered the TARDIS console room from one of the TARDIS' many hallways. They had been asleep in the TARDIS medical area recovering from having their time energy drained by Zygons. Now that they were awake, they had questions, starting with what Rose Tyler was doing here. Clara and Rose told Martha and Mickey what happened while they were asleep. Everyone, including S.H.I.E.L.D. seemed to forget that Jiaying's deadly poison was still at the bottom of the ocean and had begun contaminating fish.

* * *

London, England 2015

The TARDIS materialized at the Powell Estate, where Rose and her family used to live and where Clara Oswald was currently living. The Doctor, Clara, Danny, Jack, Rose, Martha, and Mickey all stepped out and gathered in front of the time machine to talk amongst themselves in the fresh air. The Doctor couldn't remember the last time he had so many of his companions in one place. Martha and Mickey were now all caught up on Utron, the new Avengers, Jiaying, Inhumans, the Zygon invasion, Missy, Ward, the Cyberman invasion, and the Cyber-Daleks. Martha was particularly mad to discover that the Master was still alive. Jack, Martha, and Mickey all had apartments downtown that they wanted to get back to. They wished everyone the best of luck in finding a way to stop the Cyber-Daleks and to contact them if they ever needed any help. Then, the three of them left.

"Can I speak to the Doctor alone for a minute?" Clara asked.

Danny and Rose then silently walked away to give Clara and the Doctor some space.

"What is it Clara?" The Doctor asked.

"It's Danny." Clara said. "I love him."

"And you want to stay with him permanently and stop traveling." The Doctor said. "I figured this would happen."

Clara started to shed a few tears, but smiled.

"I loved every single second in the TARDIS." Clara said.

"I know." The Doctor said. "You deserve to be happy. Be with Danny. I'm going to find Gallifrey and help Rose with the Cyber-Daleks. I have plenty of things to do."

"This isn't goodbye." Clara said. "I will see you again. Who knows? We may even have another adventure or two down the road."

"I'd like that." The Doctor said.

Clara then joined hands with Danny. They looked at each other and smiled as they walked away towards Clara's apartment.

"Where are they going?" Rose asked.

"It's just you and me again for now." The Doctor said. "I suppose we should get started. We need to find a way to get you back to your universe and to defeat the Cyber-Daleks once you get there."

* * *

New Avengers Facility, United States 2016

It had been one year since the Cyberman invasion. The Avengers now had their own secure base in upstate New York. It had only been breached once by Scott Lang, aka Ant-Man so that he could use a special device to help stop an evil madman in San Francisco back in 2015. Hawkeye and Iron Man had taken a step back from the Avengers. Thor returned to Asgard and the Hulk was still missing. Captain America and Black Widow had been working hard the last year to train the newest Avengers: War Machine, Falcon, Scarlet Witch and Vision. Towards the end of 2015, they teamed up with the Daredevil in New York City as well as Clara Oswald and some of the Doctor's other companions to save the city from another alien threat. Now, the new Avengers were all standing in the field next to the facility on a sunny morning. They were going through a routine training exercise. However, something in the sky caught they attention. There was a flashing blue light for a brief moment. When the light disappeared. There was something new hovering in the air and it was dangerous. Captain America and Black Widow heard Rose Tyler's detailed story and knew what this silver, metallic creature was. A Cyber-Dalek had just escaped from the parallel universe and was preparing to attack the Avengers.

* * *

 _THE END. Thank you all so much for reading! As you may have guessed, the story will continue in_ **The Fight for Earth 3: Rise of the Cyber-Daleks** _. Missy and Thanos have a partnership that will involve new dangers for planet Earth. The Cyber-Daleks also become a threat to the planet. Coulson's S.H.I.E.L.D. team, in addition to its own new problems, must work with the Doctor, a companion or two of his, and the Avengers to save the planet once again. However, this time the threat is much more severe than anything they faced before in the past. There will be new challenges, characters, places, and aliens. It's going to be great. Before reading that, I advise you to read a spinoff story called_ **The Time of Heroes.** It is _a continuation of the story after the events of The Fight for Earth 2: Aliens and Avengers (see my profile for the order in which stories should be read). The Time of Heroes is a crossover between Doctor Who and the Marvel/Netflix series Daredevil. You may have noticed that the last paragraph alludes to an adventure between Daredevil, some of the Avengers, and some of the Doctor's companions involving an alien attack in New York City. The Time of Heroes will show this adventure, which takes place before the Cyber-Dalek appears at the Avengers Facility. While it is not strictly necessary that you read it in order to understand the third fight for earth, some important events and themes from time of heroes will carry over into the third story. I hope you liked this story and I hope you'll continue to read Time of Heroes and Fight for Earth 3! Please review this story and let me know what you think! It means a lot! Thanks! :)_


End file.
